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Option 1:
Setup an item number for overdraft check
Setup an item number for bank charge
Invoice the customer for the amount of the overdraft
In your bank account, make a manual withdrawal amount to the account that received the overdraft
This will probably be your actual bank account, not the Cash on Hand where the first receipt went into
When the customer pays for the overdraft, apply it to the invoice
Option 2:
Void the original payment receipt
Transfer funds from the actual bank to the Cash on Hand bank to clear the balance
Create an invoice, item or manual, to the customer for bank overdraft fee
Enter a payment on account when the customer pays for the original invoice and the invoice for the fee