Thanks for the question. Regarding deposits, the deposit is part of the invoice transaction; there is no separating it It is always going to default to the date of the invoice. If the deposit/down payment is on a different date from the invoice, and should be recorded as such, it should be recorded in QuickBooks as a payment, not as a deposit.
I definitely understand where you are coming from. Let me see if I can clarify. The deposit field on an invoice is to record that the customer provided a deposit when the order/invoice was created. Anything other than this, should be recorded in QBO as a payment.