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.
- Navigate to the Accounting on the left panel and select Chart of Accounts
- Select the account where the payment was deposited and then click view register
- Then click Edit
- Once on the Bank Deposit Screen, select the customer's name in the Received From the column.
- In the Accounts column select Accounts Receivable
- Click Save and close.
- The payment will show up as a credit in the Receive Payments tab.