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Before matching the invoice overpayment, you'll need to record it first through Receive payment by entering the exact amount paid by the customer.
You can choose to record it as a refund or a credit (if the customer is set up to apply for future payments by default). Then, handle the customer credit or overpayment.
After, in the Bank deposit feature place the payment under the Undeposited Funds account. So that, you'll be able to deposit the funds or the received payment in the bank.
Refer to the steps below as to how to do it:
To keep your account updated, once done downloading the payment match it to the existing entry in QuickBooks. You can read this article for the detailed steps: Categorize and match online bank transactions in QuickBooks Online.
You can also record an invoice overpayment as a tip in case your customer considers it that way.
Feel free to reply to this post if you have additional questions about the customer's overpayment. I'll be willing to assist you. Have a good one!