I just got off the phone with Quickbooks support and was able to solve the problem.

By using the deposit field on the invoice, QBO will automatically record the deposit as a deposit into the bank account you've selected.

To see the details you can click at the bottom of the invoice More > Transaction Journal and from there you can see exactly which accounts were debited and credited.

As long as you selected the correct bank account that the deposit was made to, there's nothing else to do to record the payment other than when you take the final payment for the remaining balance.