We have suppliers where they make one large prepay on a purchase order. The vendor ships the product and it is received in several instances.
Order 500 units: Ship 200 units 1 month, 250 units the next month, and 50 units the following month.
The cost $2.00/unit = $,1000
The advance was $500 ($1/unit or 50%), so the first receiving we want to invoice $400, and deduct $200 ($1/unit or 50%) for the advance, then the second we want to invoice $500 and deduct $250 ($1/unit or 50%), for the advance, Last we will invoice $100 and deduct the remaining $50 ($1/unit or 50%), from the advance.

However GP will only allow us to deduct the full amount of the advance up to the invoice amount. We want ability to change the apply amount on the prepay. I have looked into other 3rd party products and cannot find anything.