Is there any way, while in Pay Bills, that you can apply a specific credit memo to a specific invoice that is being paid?

Thank you for posting here in Community @riverbendnurseri,

You can apply the credit memo in the Receive Payment window since it's a customer credit. However, you can use a vendor credit for your bills. 

Here are the steps on how to apply for a vendor credit in pay bills:

1. Go to the +New button.
2. Under the vendor column, select Vendor credit.
3. In the vendor drop-down, choose the vendor.
4. You can select either Category details or Item details and click the drop-down arrow to enter the information needed.
5. In the left part of the section, place the credit amount.
6. Click the Save and Close button.

I've also provided a screenshot for your reference.

You can apply the vendor credit in a bill that is already paid.

Here's how:

1. On the left panel, click Expenses.
2. Select the Vendors tab.
3. Click the vendor name.
4. Select the bill payment where the vendor credit needs to apply.
5. Under the Add to Bill Payment box on the right portion, click Add to enter the credit.
6. Click the Save and Close button.
7. Select Yes.

In case you need help pulling up a report on all money paid to a vendor, refer to this link: Run a report with vendor totals.

If you need further assistance, please leave a comment below. I'd be happier to help.