I do this in cash receipts entry. I enter the shortage in the "disc used" column & the amount posts to the GL we have set up for discounts. I try to catch this when I post the original payment, but it can be done anytime.
If you don't want these types of postings intermingling with discounts you officially offer, then you can still use cash receipts. Enter a zero dollar check. Enter the balance due as the "amt posted" for the invoice. Then on the next line, enter a gl posting for the same amount, but negative. Use whatever GL account is appropriate for you.
