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.