The idea behind the Paid in Full Credit Card Assist setting is straightforward. It adds a button in the Inspector Pane that, when clicked, automatically enters the difference between the balance due on your credit card and the Available for Payment “envelope.”
In effect, the Toolkit is calculating the difference between your credit card’s current account balance and how much you have allocated to pay to your credit card. Then, if you click the “Rectify Difference” button, that number is automatically budgeted to the credit card payment category.
This setting is not capable of any sort of subtlety. It does not and cannot differentiate between a Paid-in-Full card (statement balance) and a $0 balance (account balance).