Unfortunately this feature has not yet been implemented into the program, so there is not a way to enter in a negative amount, or over pay for a payable item that you have received from a vendor.
The current workaround or alternative is to use the Bank Adjustments screen to credit the dollar amount to an appropriate account. Using this method there is a Memo section that can serve as a place to indicate the reason for this adjustment.
You can also create a special account for this action by going to Accounting and then "Chart of Accounts".