Taking deposits with PayDirect

Hi, we recently started using PayDirect to give our clients the option of using the credit card function to pay their product. As we take deposits for our orders I would like to use an Order rather than an Invoice to accept the Deposit. I see no way of using PayDirect unless I create an Invoice, which means that I can't record deposits taken without turning the order it into an invoice. Am I looking at this all wrong or is there a way to use PayDirect by sending an Order to our customer? Ideally the process is Quote | Order, which needs a deposit so we can see jobs outstanding | Job completed would than create an invoice to pay the remaining amount.

I've never used this process and would appreciate any help you could provide.