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To record the fees and finance charges, you can create a Bank Deposit. You'll use an Income account if you don't have an invoice involved. However, if you have an invoice, use the Accounts Receivable. Enter the full amount and the customer's name. Add another line item for the small fees and use an Expense Account, then enter the amount as negative.
See the steps below for your reference:
You can learn more in the following article below: Deposit payments into the Undeposited Funds account in QuickBooks Desktop.
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