We turn on 'partial payments' in the global product settings, and we can accept partial payments in documents. It shouldn't be much of a stretch to turn on/off a 'Deposit Amount' line on the Form payments, where people can pay the pre-set (in global settings) deposit amount and it separates out the 'Amount Due'. This separation would also be very useful on the invoice so it's more clear that partial payment is an option.

Thanks so much!