Hi JKam,
The early payment discount on the term will always be based on the due amount. Therefore, in your case, you can have a workaround like adding the freight allowance as another line item with a negative value to lessen the due amount. Or, you can remove the terms when you record a payment, then add it as another line item in a form of a discount and put a negative amount to reduce the due amount.
If you have other questions, feel free to go back to this thread.
