Amazon Payments will attempt to charge your credit card for the amount you owe if your seller account has a negative balance at the end of a settlement period. However, the amount charged may be less than the total amount you owe if you have a credit limit imposed by your bank. Amazon Payments may continue to attempt charging your credit card until the remaining balance in your seller account is paid in full.
You can also use the Make a Payment feature to repay the balance you owe. For details, see Making a Payment.