Q: I forgot to apply a discount on an invoice when I applied the check payment. How do I remove the outstanding amount on that invoice?
A: To apply the discount after the fact go to >Transactions >Accounts receivable >Apply Payments and select the customer in question  and press >Start . Next select the Payment type (e.g. 7-Check) , and enter the reference No . For the Payment Amount  press ENTER to leave it as 0 (zero). In the Description field  enter a relevant description and press ENTER. This will take you to the Payment field . Press ENTER twice. Next, go to Options located at the top menu  and select Special Sales Code Amounts . In the following window, enter 5 in the Type field  for “Early Payment Discount”. Pressing [F2] will put the discount amount in the Amount field . Alternatively, you can manually enter the amount. Finally, press Save  then Save again .
(For larger Image: right-click-image & open in new tab)