To process a NSF Check you would need to create an Invoice Item “NSF Check” with the GL Account being your Bank account. If your company charges a fee you would to create an Invoice Item “NSF Fee”.
You would then create a new invoice, using the “NSF Check” item. By using this Invoice Item, which is pointing to your bank account, it will not reflect as a Sale in your reporting. If you are charging a fee add that to this invoice at this time.
When your client then pays this invoice it will show the payment going towards the proper GL Accounts and, again, not showing as a Sale in your reporting.