I have encountered this issue in 2 different clients, both using QB desktop, one using Pro and one using Enterprise. When a vendor bill is entered, partly with a credit, the bill doesn't disappear from the "Pay Bills" window when it is paid. What I mean is: suppose you get an invoice for $105, but if you pay the invoice right away, you only need to pay $100. I want to enter the $105 as an expense, and the $5 as a credit on the same Enter Bills screen. When I do that, then pay the bill using the Pay Bills window, the bill still appears in the Pay Bills screen next time I go to pay other bills. The only work-around I've found is to enter a bill for $105 and then a credit for the $5. If I don't do it this way, then the bill sits in the Pay Bills window forever. Note that the AP balance and the AP aging both correctly show the bill as having been paid.
Thanks for explaining what's going on. Your examples are great and I see what's going on and can help with navigating bills, bill payments, and vendor credits.
In QuickBooks Desktop, vendor credits are applied to a bill payment rather than the bill itself. So what you're describing about needing to enter the bill for the full amount and then factor the credit into the payment window is exactly correct. To review the steps, check out the in-product help article Apply credit from a vendor to a bill payment. Here's how to bring it up.
Select Help from the top toolbar.
Choose QuickBooks Desktop Help (Note: a shortcut to reach this is to press F1 on your keyboard).
Select the Help tab in the Have a Question? window.
Enter keywords such as "vendor credits" into the search bar and hit enter.
Click the title of the article to read it.
There are a number of other articles there as well that you're welcome to go over. The Pay Bills in QuickBooks Desktop article in community also goes over some of these things.
I hope that helps! Let me know if you have more questions.