You can schedule the AFT payment to "pay the amount in full every time (for credit cards or lines of credit)."  Making this selection allows the member to pay the LOC or credit card off every time a transfer is performed. (The recommended frequency with this AFT payment method is Monthly.)

For LOCs, this means pay whatever the current balance on the loan is at the time the transfer is performed. If the AFT payment amount will result in an overpayment on the loan, the transfer amount will be adjusted to the loan's current balance to avoid overpaying the loan.

Online credit cards work a little differently. Instead of looking at the current balance (CURBAL) on the loan, the AFT pays the statement balance from the most recent credit card statement. But like LOCs, if the AFT payment amount will result in an overpayment on the credit card, the transfer amount will be adjusted to the loan's current balance to avoid bringing the balance below $0.
For example, say a member’s last statement balance was $285.00. A few days later the the member transferred $25.00 to the account, making the new current balance $260.00. When the AFT is processed it will only pull $260.00 (the loan’s current balance) not $285.00.
 
Note: Keep in mind that for credit cards, the statement balance is refreshed each month, so the timing of statement generation compared to the AFT transfer date might have a bearing on what the payment amount will actually be.