Thanks for the detailed reply. This does seem to be a better way than using a journal entry. My last question though is regarding the recording of the expense details as a negative on the bank deposit.

In terms of the "Received From" and "Category/Account", do I match what the expense has since the expense has already been created? So if the expense has the Payee "Test Customer" and the Category "Bank Account", will the bank deposit line for it be the same? That won't cause duplicate transactions?