Common 1099 processing questions

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Important information

Federal/state/local forms and tax tables are released with Accounting CS updates via CS Connect. We recommend that you periodically check for application updates, and take advantage of the following resources, to determine when the forms and tax tables will be available.

1099 processing

Prior to processing

You must be licensed for Accounting CS Payroll Compliance to process 1099 forms. Contact our Customer Service team for more information.

  • Vendor List – Detailed. To verify that vendor information is up to date, mark the 1099 Properties checkbox (unmark Distributions and Payment Preferences) in the Regions to Include section.
  • 1099 Activity. To verify 1099 types and amounts, select Current year (or Prior year, if applicable) as the period to process in the Date section.
  • Verify vendor TINs with the Internal Revenue Service (optional). See Verifying vendor TINs with the IRS.

There are a couple of ways to enter 1099 information for clients for whom you do not provide live payroll services.

Processing Form 1099

  1. Choose Actions > Process Payroll Tax Forms.
  2. Select 1099 from the drop-down list in the Form type field, select the applicable 1099 type from the 1099 type field, and then select the year.
  3. Click the Refresh button to populate the Form Selection section. Note that you can filter the number of clients listed in the Form Selection section by using the filter options.
  4. For each client, mark the checkbox for the forms you want to include and then click the Process Selected button.

For step-by-step information about how to process 1099 forms, see Workflow - Processing 1099 forms.

You can preview all available copies.

The red scannable forms are still required. Because the IRS did not release specifications to produce black-and-white facsimile Copy A or 1096 forms, we cannot offer this print option.

No, the application will only process and print forms that contain information. If you need to order blank 1099 forms, see Ordering Forms W-2, 1099, and 1095-C for additional information.

You can print the following 1099 forms and the corresponding 1096 form.

1098

1098-C

1098-E

1098-T

1099-A

1099-B

1099-C

1099-DIV

1099-G

1099-INT

1099-MISC

1099-OID

1099-PATR

1099-R

1099-S

1099-SA

5498

5498-SA

W-2G

 

 

  1. Click the Print Options button.
  2. In the Filing Method Selection section, select Per client selection. Any other selection in this field is a global override for all clients. Show me
    PrintOpt1099method
  3. Click OK to save your changes.
  4. In the Form Selection grid, you are now able to change the Filing Method selection on a per client basis. Note that the filing methods default to whatever is set up for the forms on the Payroll Taxes tab of the Setup > Clients screen.

There are a few possible answers to this question. See the Why am I getting a message that says there were no 1099s to print? topic for detailed information.

Accounting CS supports the printing of only 1099-MISC forms with Box 7 for non-employee compensation type employees. To print Form 1099-MISC for an employee, follow these steps.

  1. Choose Setup > Payroll Items and set up a Calculation Special Type Nonemployee compensation pay item.
  2. Choose Setup > Employees and add an employee with Independent Contractor selected in the Type field. This makes nonemployee compensation pay items available for selection for this employee in the Setup > Employees > Payroll Items tab and makes the employee available for 1099 processing.

Overrides remain indefinitely (quarter to quarter and year to year) until they are manually cleared.

  • You can clear overrides in the Recipient Data and Client Data tabs of the Actions > Edit Payroll Tax Forms screen by using the buttons at the top of the tab.
    • Clear Override. Clears the override in the field in which your cursor is placed.
    • Clear All Overrides. Clears all overridden fields displayed on the active tab. (Overridden fields are displayed in red or with a red outline.)
  • You can clear recipient overrides prior to previewing or printing the form by marking the Clear recipient overrides checkbox in the Actions > Process Payroll Tax Forms screen.

If amounts from the transactions you entered are not displaying on the Form 1099, verify the following settings.

  1. Choose Actions > Enter Transactions and highlight a transaction for the vendor.
  2. Verify either that the Handwritten / Check # checkbox is marked, or that the status of the transaction (located above the Add button) is Printed.
  3. Verify the transaction date is in the same year that you are reporting the 1099.
  4. In the Transaction Detail section, click the Distributions tab and verify that there is a 1099 form and box selected in the 1099 column.
If you are unable to edit a transaction, review Possible reasons why certain transactions cannot be modified.

To determine why the amounts are incorrect, try the following suggestions.

  • Print the 1099 Activity report to verify the 1099 types and amounts are correct for the vendor.
  • Check to see if there are overridden amounts from the previous year that need to be cleared in the Recipient Data tab of the Actions > Edit Payroll Tax Forms screen.

There are two possible areas to review and/or update.

Vendors

  1. Choose Setup > Vendors and then click the 1099 Properties tab.
  2. Verify that the One Form per Transaction checkbox is not marked.

Transactions

  1. Choose Actions > Enter Transactions and then highlight a transaction that has 1099 distributions.
  2. Click the Ellipsis button next to the 1099 distribution and verify that the One 1099 per transaction checkbox is not marked.

This typically happens when a vendor was previously set up to receive a 1099 but no longer does. Follow these steps to remove the 1099 settings for that vendor.

  1. Choose Setup > Vendors.
  2. Select the vendor and click the Edit button.
  3. On the Main tab, select 1099 Recipient from the Vendor type.
  4. On the 1099 Properties tab, click the area to the left of the Form Selection field to highlight the whole row.
  5. Click the Red X button, or press the Delete key on your keyboard.
  6. Click Enter to save your changes.

    Note: If amounts on the 1099 form are from transactions that were entered as 1099 items, follow these steps to remove the 1099 items.

    1. Choose Actions > Enter Transactions and highlight the transaction for the vendor.
    2. In the Transaction Detail section, click the Distributions tab and highlight the 1099 item.
    3. Press the delete key on your keyboard to remove the 1099 item from the transaction.
    4. Save your changes by clicking Enter key.

    If you are unable to edit a transaction, review Possible reasons why certain transactions cannot be modified.

  7. Click Edit in Setup > Vendors to make the next change.
  8. On the Main tab, change the Vendor type field back to the correct type.

If the 1099 forms are not displaying, verify the following areas.

Hidden forms

  1. Choose File > Process Client Forms.
  2. Click the Print Options button.
  3. Within the Copy to Hide section, unselect the forms you would like to view.

Note: Forms can be hidden within Process Payroll Tax forms, click on the Print Options and unselect the forms you would like to see listed.

Active date

  1. Choose Setup > Clients.
  2. Verify the Active date, in the Client Information section of the Main tab, is within the tax year for the tax forms you are processing. Example, for 2018 tax forms, the Active date must be prior to 2019.

The 1099 printing threshold amount is an amount below which you do not want to print 1099s for a client. You can set up the printing threshold amount in the Form 1099 Details dialog or change it at print time in the Print Options dialog for Form 1099.  

There are a few possible reasons that the application might ignore the 1099 printing thresholds that have been set up. Use the following steps to verify that these options are not selected. 

When you add the vendor

  1. Choose Setup > Vendors and then click the 1099 Properties tab.
  2. Clear the Always Print Form checkbox, if it is marked.

If you enter transactions for this vendor:

  1. Choose Actions > Enter Transactions.
  2. Highlight one of the transactions for this vendor in the list.
  3. Click the Ellipsis button next to the 1099 distribution to open the Form 1099 Details dialog.
  4. Clear the One 1099 per transaction checkbox.

When you select the Print Options button in Edit Payroll Tax Forms (choose File > Process Client forms) or in Process Payroll Tax Forms.

  1. Click the Print Options button.
  2. Clear the Ignore per item threshold overrides option, if it is marked.
  1. Choose Actions > Edit Payroll Tax Forms.
  2. Select 1099 from the drop-down list in the Form type field, select the applicable 1099 type from the 1099 type field, select the year, and then click the Refresh button.
  3. Select Copy A in the Form field, and then click the Recipient Data tab.
  4. Right-click in the grid area and choose Deselect all.
  5. Mark the checkbox for the recipient you need to re-print.
  6. Click the Process Client Forms button on the toolbar or choose File > Process Client Forms.
  7. In the Process Client 1099 Forms dialog:
    • Unselect Print All Recipients.
    • Mark the checkboxes next to the forms you want to process.
    • Specify the filing methods, and print options for the forms.
  8. Click the Process Selected button.

Note: If the Always Print Form checkbox is marked on the Setup > Vendors screen on the 1099 Properties tab, a 1099 will print for that vendor regardless of any other settings.

For further details, see Reprocessing Internet/magnetic payroll tax forms

Editing Form 1099 amounts in information

You may need to do one or more of the following:

For live 1099 processing, follow these steps:

  1. Choose Actions > Enter Transactions.
  2. Highlight a transaction with a 1099 distribution.
  3. In the Transaction Detail section, click the Ellipsis button to the right of the distribution row.
  4. In the Form Label 1099 Details dialog, enter the description, address, City, State, and Zip.

    The Description field will not display on the 1099-S. If you need the Description of the property included in Box 3 on the 1099-S, you can add the variable [TaxForm.1099S.DescriptionofProperty] to the form through the Layout Editor.

  5. Select the closing date in Date of closing drop down to populate Box 1.

For after-the-fact 1099 processing without transactions entered in the application, follow these steps:

  1. Choose Actions > Edit Payroll Tax Forms.
  2. Filter for Form type: 1099, then 1099-S, the appropriate year and click Refresh.
  3. Select Copy A from the Form drop-down menu.
  4. Click the Recipient Data tab and locate the vendor for whom you need to mark these checkboxes.
  5. Using the horizontal scroll bar, scroll to the right.
  6. Enter the information into Box 3 Description, Box 3 Address, Box 3 City, Box 3, State, and Box 3 Zip.

    Box 3 Description will not display on the 1099-S. If you need the Description of the property included in Box 3 on the 1099-S, you can add the variable [TaxForm.1099S.DescriptionofProperty] to the form through the Layout Editor.

  7. Enter the closing date in Box 1 Date of Closing.

For live 1099 processing, follow these steps:

  1. Choose Actions > Enter Transactions.
  2. Highlight a transaction with a 1099 distribution.
  3. In the Transaction Detail section, click the Ellipsis button to the right of the distribution row.
  4. In the Form 1099 Details dialog, mark the 2nd IRS notification incorrect recipient TIN and/or the FATCA filing requirement checkboxes.

For after-the-fact 1099 processing without transactions entered in the application, follow these steps:

  1. Choose Actions > Edit Payroll Tax Forms.
  2. Filter for Form type: 1099, then 1099-MISC, the appropriate year and click Refresh.
  3. Select Copy A from the Form drop-down menu.
  4. Click the Recipient Data tab and locate the vendor for whom you need to mark these checkboxes.
  5. Using the horizontal scroll bar, scroll all the way to the right.
  6. Mark the checkbox in either the 2nd TIN Not and/or the FATCA column, as appropriate.

Layouts, variables, and display options

To go back to the original (default) form layout, choose File > Layout Designer, open the modified layout, and then choose File > Restore Default.

You will need to add the DBA variable to the different 1099 files you are processing. 

  1. Choose File > Layout Designer.
  2. In the Layout Designer, click the plus sign next to the 1099 Forms folder to expand it, and then expand the folder for the specific year.
  3. Double-click the form layout to open it. For example, if you need to make changes to the 1099-MISC Copy A form, double click the 1099MISa form to open it.

    Note: To edit 1099 Miscellaneous Copy A, you would make changes to the 1099misca form. 1099MIS represents the name of the form and a represents the copy of the form. This change will affect only Copy A. If you want to adjust the alignment for the other copies, you need to make the same adjustments to those copies — for example, to 1099MISb or 1099MISc, etc. If you need to undo your modifications on the 1099 form and return to the original (default) form, choose File > Restore Default when the form is displayed.

  4. In the RECIPIENTS name box on the form, click on the [TaxFrom.1099Recipient.Name] variable and use the up arrow on your keyboard to move the existing variable up just a bit to make more room for the DBA variable you will be adding.
  5. Within the Design Tools section on the right, choose Variables.
  6. Click the plus sign next to Tax Form and then click the plus sign next to 1099 Recipient.
  7. Highlight DBA Name and drag it into the RECIPIENTS name box under the [TaxForm.1099Recipient.Name] variable. Use the arrow keys on your keyboard to fine-tune the alignment of the variable.
  8. Choose File > Save to save your changes.

    Note: You cannot save the 1099 forms as a new layout with a different name. Only those vendors that have a DBA name entered would be affected by this change.

To avoid having to make the alignment adjustments that are often needed when you use preprinted laser forms, you may want to consider filing via electronic file submission for Federal Copy A. Additionally, print the black-and-white forms to unperforated paper and generate facsimile forms from Accounting CS for all other copies.

To adjust the alignment of Form 1099-MISC Copy A, you need to perform the following steps.

  1. Choose File > Layout Designer.
  2. In the Layout Designer, click the plus sign next to the 1099 Forms folder to expand it, and then expand the folder for the specific year.
  3. Double-click the 1099MISa layout to open it.
  4. Adjust the alignment using either of the following methods.
    • To adjust the entire form, choose Edit > Select All (or press CTRL+A on your keyboard) and then use the directional arrows on your keyboard to adjust the document as needed.
    • To adjust the alignment of an individual field, click inside the field and then use the directional arrows on your keyboard to move the field to the desired location.
  5. Choose File > Save to save your changes.

Note: 1099MIS represents the name of the form and a represents the copy of the form. This change will affect only Copy A. If you want to adjust the alignment for the other copies, you need to make the same adjustments to those copies — for example, to 1099MISb or 1099MISc, etc. If you need to undo your modifications on the 1099 form and return to the original (default) form, choose File > Restore Default when the form is displayed.

If you added a variable or changed something in the layout, be sure that you have also changed each copy of the layout. For example, if you changed the variable in RECIPIENTS identification number box to display the last four digits, you also need to add that variable to every other 1099 layout listed for that year to have the change affect all copies of the form.

In addition, make sure you did not add text variables and then attempt to print using the preprinted paper form options. By design, the preprinted filing method suppresses all text variables.

Note: 1099MIS represents the name of the form and a represents the copy of the form. This change will affect only Copy A. If you want to adjust the alignment for the other copies, you need to make the same adjustments to those copies — for example, to 1099MISb or 1099MISc, etc. If you need to undo your modifications on the 1099 form and return to the original (default) form, choose File > Restore Default when the form is displayed

There are two ways to remove the client copy image from payroll tax forms.

Remove on a per client basis

Within Edit Payroll Tax Forms

  1. Go to Actions > Edit Payroll Tax Forms.
  2. Select the form type, year, etc.
  3. Choose File > Process Client forms.
  4. Select the forms you need to print.
  5. Click on Process Selected button.
  6. Select Filing copy.
  7. Click OK.

Within Process Payroll Tax Forms

  1. Go to Actions > Process Payroll Tax Forms.
  2. Select the form type, year, etc.
  3. Select Client and forms you need to print.
  4. Click on Process Selected button.
  5. Select Filing copy.
  6. Click OK.

Remove globally for all client payroll tax forms

This process will disable the application's default behavior of printing a watermark on all client copy forms (forms for which the Client copy checkbox is marked in the Print dialog).

  1. Go to the Preferences tab of Setup > Firm Information > Firm.
  2. In the Payroll Tax Forms section select Disable watermark on client copy forms.
  3. Click OK.

The client’s copy is always displayed when previewing a payroll tax form. Selecting to disable watermark on client copy form will remove the CLIENT COPY watermark from the preview screen.

See also: Setting up and processing form 1099 for recipients

The recipient's identification number is truncated on all 2018 1099 forms except Copy A (Federal) and Copy 2 (State). Following IRS regulations, the first five digits of the nine-digit number has been replaced with Xs. See the Masking Recipient TINs on Form 1099 topic for detailed information to edit prior tax year forms.

Per the IRS general instructions for certain information returns, the account number may be a required field. Accounting CS populates this field automatically with a unique number for filing purposes.

If you wish to remove the account number from the 1099 form, use these steps:

  1. Choose File > Layout Designer and open the 1099 Forms and year folder.
  2. Double-click the form that you are processing to open it.
  3. Click the variable in the Account number box and then press the Delete key on your keyboard.
  4. Choose File > Save and then close the Layout Designer window.
  5. Preview or process the form and there will no longer be an account number displayed.

Other

Within Edit Payroll Tax Forms

  1. Choose Actions > Edit Payroll Tax Forms.
  2. Select 1099 from the drop-down list in the Form type field, select W‑2G from the 1099 type field, and then select the year.
  3. Click the Refresh button and select the form you wish to view.
  4. The Recipient Data tab will list the vendors with 1098 associations.

Within Process Payroll Tax Forms

  1. Choose Actions > Process Payroll Tax Forms.
  2. Select 1099 from the drop-down list in the Form type field, select W‑2G from the 1099 type field, and then select the year.
  3. Click the Refresh button to populate the Form Selection section. Note that you can filter the number of clients listed in the Form Selection section by using the filter options.
  4. For each client, mark the checkbox for the forms you want to include. 

At this time, Accounting CS does not support filing instructions for 1099 and 1096 forms. This is a suggestion in our Accounting CS Ideas Community. See Printing filing instructions for payroll tax forms for standard filing instructions other than 1099s.

At this time, Accounting CS does not support printing Instructions for Recipient on the back the recipient’s copy of Form 1099. This is a suggestion in our Accounting CS Ideas Community. See IRS instructions for W-2/1099 recipients to view or print the Instructions for Recipient separately.

Vendors must meet the following conditions for Accounting CS to print a 1099 form.

  • The vendor type selected in the Main tab of the Setup > Vendors screen must be 1099 Recipient.
  • At least one form and one box must be selected in the 1099 Properties tab on the Setup > Vendors screen.

Independent Contractors must meet the following conditions for Accounting CS to print a 1099 form.

  • The employee type selected in the Main tab of the Setup > Employees screen must be Independent Contractor.
  • If you will be entering transactions for this employee, a payroll item with the special type Nonemployee compensation must be active on the employee.

If your firm uses the Employee Self-Service feature, and you want to send an electronic copy of the 1099-MISC form to the Employee Self-Service portal of independent contractor employees at form print time to avoid processing the 1099 forms a second time, you have two options.

  • In the Payroll Taxes tab of Setup > Clients, mark the Send 1099-MISC to Employee Self-Service checkbox in the Independent Contractor section of the 1099 Additional Information dialog. The electronic copy of the 1099-MISC form will be sent to the Employee Self-Service portal for all independent contractor employees every time you print 1099-MISC forms for the selected client, unless you have only Copy A selected during processing.
  • While processing your payroll tax form, mark the Send to Employee Self-Service (Independent contractors only) checkbox in the Print Options dialog for Form 1099-MISC. The electronic copy of the 1099-MISC form will be sent to the Employee Self-Service portal for all independent contractor employees. This checkbox affects only the forms currently being printed, regardless of what is selected in the 1099 Additional Information dialog of the Setup > Clients screen.

 See Also: Employee Self-Service overview

1096 Processing

  1. Open the Additional Information dialog by clicking the Additional Information button in one of the two following locations.
    • The Forms section (next to the Signature) of the Payroll Taxes tab in the Setup > Clients screen.
    • The top of the Actions > Edit Payroll Tax Forms screen when the 1099 Form is selected.
  2. Enter or select the appropriate information in each field.
  1. Open the Additional Information dialog by clicking the Additional Information button in one of the two following locations.
    • The forms section (next to the Signature) of the Payroll Taxes tab in the Setup > Clients screen.
    • The top of the Actions > Edit Payroll Tax Forms screen when the 1099 Form is selected.
  2. Select something other than None from the drop-down menu in the Signature field.
  3. Mark the Suppress date checkbox.

The Form 1096 is not listed separately from the 1099 Copy A line item in the Process Internet/Magnetic Files screen because the IRS indicates that the Internet file should contain both the Copy A and the 1096 information.

Internet filing

The application enables you to create a Form 1099 file that you can upload to the IRS electronic filing program, Filing Information Returns Electronically (FIRE). In the Actions > Process Payroll Tax Forms screen, change the filing method for the Copy A to Internet and then click the Process Selected button to add your client's data to a batch file. Follow these steps to verify the contents of your file.

  1. Choose Actions > Process Internet/Magnetic Files.
  2. Select the appropriate file and click the Preview Selected button.
  3. Click the Create Files button to create the file and store it in the file location listed at the bottom of the screen.
  4. Upload the file via the IRS FIRE program.

For information about electronic filing of 1099s or to determine whether you must enroll or register to file electronically, visit the IRS website at www.irs.gov/e-file-providers/filing-information-returns-electronically-fire. If you have problems with or questions about sending the file using the IRS FIRE program, please contact the IRS.

There are specific 1099 file types that can be processed for each state using Accounting CS. See the 1099 files overview topic for detailed information.

Although Accounting CS allows you to maximize your efficiency by batch processing many clients at the same time, with the 2016.4.0 update there is an easy way to select which clients to process Internet/Magnetic files for.

  1. Perform the steps in the Processing 1099 forms for all recipients of one or more clients section in the Printing 1099 forms topic
  2. Choose Actions > Process Internet/Magnetic Files, and then click the plus sign next to Federal 1099-MISC Copy A.
  3. Mark the checkboxes for the client you want to create a single file for and then click Create Files.

Accounting CS will create a folder in the location specified on the Process Internet/Magnetic Files screen for each time you perform these steps. The folder will be named "Batch File X" where X is the next batch number available.

No, you will need to reprocess the 1099 forms in the Actions > Process Payroll Tax Forms screen for that client. If you are prompted to overwrite the existing file, do so. You can then access the updated file in the Manage Files dialog, accessed from the Actions > Process Internet/Magnetic Files screen.

There are a few possible answers to this question. See the Nothing appears in the Process Internet/Magnetic Files screen topic for detailed information.

There are a few possible answers to this question. See the Nothing appears in the Process Internet/Magnetic Files screen topic for detailed information.

When the Require internet/magnetic file creation from file preview checkbox is marked in the Preferences tab of the Setup > Firm Information > Firm screen, you will need to preview the files and then create them from the Preview screen.

The Following are some solutions to error message that may display when you attempt to create the internet file.

You must enter an ID.

  1. Choose Actions > Process Internet/Magnetic Files.
  2. Click the Transmitter Information button.
  3. In the Federal 1099 section, enter your 5-digit Transmitter Control Code provided by the IRS.

You must enter a Transmitter Contact Name, Phone, and/or Email.

  1. Choose Actions > Process Internet/Magnetic Files.
  2. Click the Transmitter Information button.
  3. In the General section of the Transmitter Information dialog, select a staff member from the File Contact drop-down list.

Note: If you have an Alternate Preparer Block license, choose Setup > Firm Information > Firm and complete the Alternate Firm and Alternate EIN/SSN fields on the Main tab.

If there are no entries in the drop-down list, close the dialog and choose Setup > Firm Information > Staff.

  1. Select a staff member who is a payroll form preparer and then click the Edit button.
  2. In the Preparer Information section, verify that the Payroll form preparer checkbox is marked, and the PTIN and Third-party designee PIN (if applicable) are entered.
  3. In the Phone and Fax Numbers section, verify that there is a phone number entered in the Business field and that there is an email address entered in the Email Add any missing information.
  4. Make the same changes for any other staff members that should be included in the list of payroll form preparers.
  5. Press Enter to save your changes.
  6. Choose Actions > Process Internet/Magnetic Files and then click the Transmitter Information button.
  7. In the General section, select the appropriate staff name, which should now display in the drop-down list.

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