Discounts and Fees
If you need to apply an additional fee or discount to a merchant's deal, you can do so by adding a transaction and selecting either type:
Adding a discount will reduce the total amount outstanding for the deal, where as adding a fee will increase the amount outstanding.
In the event that a merchant has made an overpayment and you need to refund the merchant, you should create a transaction with a negative amount and denote it as being a refund.
This will reduce the amount repaid on the deal and help balance out your numbers. Adding a discount in this case would not help since it only affects the amount outstanding.