Processing New York state payroll tax forms for electronic filing

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Accounting CS offers the ability to electronically file the New York state Form NYS-45 and the NYS-1 payment voucher. Use the following steps to set up clients for NY e-filing and processing. (Mandatory electronic filing for New York withholding began on April 30, 2015).

Client setup

  1. Choose Setup > Clients and then highlight the appropriate client.
  2. Click the Edit button, and then click the Payroll Taxes tab.
  3. Verify that the following information is entered:
    1. Unemployment ID (must be 7 digits long)
    2. Withholding ID

      Note: The first 9 digits of the Withholding ID must be the same as the Federal EIN. The last two digits are your extension code (if applicable).

    3. Unemployment rate
  4. In the Taxes grid, verify that each of the New York withholding items is assigned to an Agent.
  5. In the Forms grid, verify the Filing Method for the NYS-45 is Electronic or Electronic with payment, and the Do Not File checkbox is cleared.
  6. Click the Additional Information button next to New York and complete all of the fields.

See also: Setting up client payroll tax information

Bank Account Setup

  1. Choose Setup > Bank Accounts.
  2. In the Identification section of the Main tab, enter the bank account holder name in the Account holder name field.
  3. Click Enter to save the bank account information.

Vendor setup

Electronic with filing method

  1. Choose Setup > Vendors, highlight the NYS Income Tax vendor and then click the Edit button.
  2. On the Main tab, in the Payment Preferences section, select the appropriate bank account.
  3. Verify that the Method field is set to Electronic and an authorization number is entered.

Note: Your authorization number is a 6 digit number provided to you by New York State when you enroll for EFT filing with the PrompTax program.

Electronic filing method

  1. Choose Setup > Vendors, highlight the NYS Income Tax vendor and then click the Edit button.
  2. On the Main tab, in the Payment Preferences section, select the appropriate bank account.
  3. Verify that the Method field is NOT set to Electronic.

Other setup items

  1. Choose Actions > Process Electronic Forms and then click the Transmission Information button.
  2. Enter the applicable information in the General, Federal, and New York sections.

    Note: In the Reporting Agent PIN field, you'll need to enter a 10-digit, numeric PIN (of your choice) to use as the firm's electronic filing signature. This PIN is not assigned by the state, but it is required. Your electronic files will be rejected if this field is left blank.

  3. Choose Setup > Firm Information > Staff and then select the payroll form preparer.
  4. Verify that the following information is entered:
    • Title
    • Business address
    • Business phone number
    • Email address
    • PTIN and Third party designee PIN (if applicable)

Processing Form NYS-45

  1. Choose Actions > Edit Payroll Tax Forms.
  2. Filter for Form type: Reconciliation, mark the Quarterly checkbox, and select the appropriate quarter and year. 
  3. Click the Refresh button and then select NY in the Jurisdiction field and NYS-45 from the Form field.
  4. Review the automatically filled in fields, and enter any information into fields marked with a red triangle.
  5. Address any diagnostics displayed on the bottom of the screen.
  6. Choose Actions > Process Payroll Tax Forms.
  7. Filter for Form type: Reconciliation, mark the Quarterly checkbox, and select the appropriate quarter and year.
  8. Click the Refresh button.
  9. Click the plus sign next to the client to see the available forms.
  10. Mark the checkbox next to NYS-45 and verify that the filing method is Electronic or Electronic with payment.
  11. Click the Process Selected button.
  12. In the Print dialog, make your output selections, with the Filing copy checkbox marked. Note that nothing will physically print unless the Client copy checkbox is marked.
  13. Choose Actions > Process Electronic Forms and mark the checkbox next to the forms you are ready to transmit.
  14. Click the Transmit Forms button to send the NYS-45 and NYS-1 information to the state. If your filing method was set to Electronic with payment, the liability will also be marked as closed.

See also: Open liabilities do not equal balance due

Processing Form NYS-1

The application automatically generates Form NYS-1 when the following criteria are met:

You can make payments without processing form NYS-45. Simply print the liability payment on the Print Checks screen, and then you'll see the NYS-1 form available for transmission on the Process Electronic Forms screen.

Re-processing a rejected Form NYS-1

If you file NYS-1 and it is rejected, use the following steps to re-file after you make any necessary corrections.

  1. Choose Actions > Enter Transactions.
  2. Locate the NYS-1 payment in the list of transactions, and then click on it to highlight it.
  3. Click the Delete button.
  4. Choose Actions > Process Electronic Forms.
  5. Click the Manage Electronic Forms button.
  6. Use the filters to locate the rejected NYS-1 form.
  7. Mark the checkbox for the form, and then click Remove Selected.
  8. Choose File > Print Checks or Actions > Manage Impound Payments and re-process the payment.
  9. Choose Actions > Process Payroll Tax Forms and re-process the NYS-1 form (or NYS-45, whichever applies).
  10. Choose Actions > Process Electronic Forms and re-transmit the form.

Related topics

E-filing state and local payroll tax forms

E-file error rejection codes for 94x forms and state forms

Workflow - Processing payroll tax reconciliation forms

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