Hi there, @mechanicalflower.

Thanks for actively responding. I appreciate you for following the steps provided by my colleague, @IntuitLily, and @IamjuViel. 

Looking at your screenshot, it looked like the bill associated with it was deleted. Since this isn't true to you, you should see an open bill for this in the Pay bill section.

Now, let's check the box for the unpaid bills to show the available credits as shown in the screenshot below:

Then, use it to pay the bill as shown in the screenshot below: 

This will now link the cleared checks to your bill, and marked as paid. 

For future reference, read through these links to learn more about bill payments in QuickBooks Desktop:

• Pay bills in QuickBooks Desktop. It has a basic guide on how to apply the corresponding discount or credit for each payment you're going to make. 
• Use QuickBooks Bill Pay. This helps you pay your bills directly in QuickBooks Desktop and automatically records your payment so you'll have an accurate report.

Know that we're always delighted to help in any way we can if you have more questions. Stay safe. 

Mark the post that answers your question by clicking on "Accept as solution".