In the 4-2 A/P invoice module the discount should be in the discount field that is in the bottom left and the original invoice price should be entered into the price column. This will show the pre discounted invoice amount as the "invoice total".

When using the 5-3-1 "select invoices to pay" screen the amounts should show as followed:

Invoice total - Original invoice amount
Net Due - Original Invoice amount less any retentions
Discount - The amount of the discount to be applied
Set to pay - The amount the check/payment will be made to the vendor. so, the net due less the discount amount.