If a bill has multiple chartfield lines, and a customer pays one line partially and the rest in full

We had a bill that had three chartfield lines, totally $41,000. The customer paid, but only paid $40,000, and indicated the reduction was from the third line of the bill. In the payment worksheet, there doesn't appear to be a way to apply parts of a payment to specific lines--you can add multiple lines, but when you try to select a specific line, it only shows you the whole bill, not line numbers. We ended up doing a credit/rebill, but it seems there must be a way to apply a partial payment to a specific line. We've applied partial payments