You can manually apply a bill payment to your vendor, Jeff.
To begin with, is the vendor ACH payment processed online? If so, the option to apply the credit is unavailable, as QuickBooks will automatically pay the bill payment.
If it's not processed online, you can manually apply the credits to a vendor. Here's how:
- Click on the + New button.
- Choose Pay Bills.
- From the list, select the bill related to your vendor. You'll see the available credits for this vendor in the Credit Applied field.
- Apply the necessary credit and enter the required details.
- Then click Save and Close.

For more information, refer to this article: Enter vendor credits and refunds in QBO.
Also, check out this article to learn how to generate your vendor payments or totals: Run a report with vendor totals.
Feel free to click Reply below if you have further concerns about handling credits.