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From the Actions > Manage Payments screen, choose Edit > Options and mark the Allow multiple payments per vendor checkbox. This changes the Pay checkbox to a drop-down list where you can now designate which payables to pay with which check.

For example: I have three payables. Two should be on the same check and one by itself. I will select Pay 1 for the first two items and Pay 2 for the payable that should be paid by itself.

Note: Selecting Pay 1 for two different vendors will still produce a check per vendor.

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