Good afternoon, @Jdusten78.
Welcome to the Community!
QuickBooks Desktop sometimes "remembers" the last way you filled out a form rather than looking at the customer's specific file.
Go to Edit > Preferences > General. On the My Preferences tab, look for "Automatically remember account or transaction information."
If it is checked, uncheck it, click OK, restart QuickBooks, and then re-enable it. This clears the "local memory" of how you last entered a payment and can force it to look at the customer's default profile again.
Please come back and let me know how these steps worked. I'm only a post away if you need me again. Take care!