Here is a simple means to solve this problem.
1. Match payment to invoice from bank matching system
2. Add Expense for the bounced payment you see in matches, open expense and flag it as a BILLABLE EXPENSE to the customer
3. Open the original invoice, click the little arrow on right side of screen
4. Add Billable Expense to the original invoice
5. Add NSF line item to the original invoice
6. Original invoice now shows original items, day, times and payment made AND new items for bounced cheque and NSF fee
7. Save and Re-Send to customer
This process shows the real flow of monies and keeps the books and bank matches aligned correctly and is done in 2 minutes.