How do I record an NSF check returned on a payment made and applied to a customer invoice in accounts receivable?

I usually record it using a general journey entry so follow these steps:

To enter by Journal Entry:

1. Click the "+" icon and choose Journal Entry.
2. Enter the date the check bounced.
3. In the Account column, select Accounts Receivable.
4. Under Debit, enter the amount of the bounced check.
5. Under Memo, enter a notation explaining the reason for the journal entry.
6. In the Name column, select the customer name.
7. On the second line, in the Account column, select the bank account.
8. The credit and memo will enter.
9. Click Save.

To change the first payment to apply to the journal entry:

1. From the left navigation menu, click Customers/Invoicing
2. Find your customer's and and click it. 
3. In the Transaction section, locate the Payment for the bounced check, double-click if to open it.
4. Uncheck the Invoice it was applied to, and check the Journal Entry.
5. Click Save.

Hope this helps

Tracy Collins-Collins Bookkeeping