When receiving a customer's payment, you'll need to use the Receive Payment option instead of recording it as a Bank Deposit. This will ensure that the invoice can be marked as paid in QBO.
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Navigate to the Accounting on the left panel and select Chart of Accounts
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Select the account where the payment was deposited and then click view register
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Then click Edit
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Once on the Bank Deposit Screen, select the customer's name in the Received From the column.
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In the Accounts column select Accounts Receivable
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Click Save and close.
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The payment will show up as a credit in the Receive Payments tab.
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