If you're using the QuickBooks Online version, you can still use the Journal Entry feature if you need to clear balances on your Accounts Payable. It would still be best to consult with your accountant to make sure what's best for you and your business.
If this is for a customer with overpayments, you can use the credit column for the accounts payable. To apply the journal entry to the existing debit or credit, you can use the Receive Payment feature.