In earlier experimental versions a "request deposit" feature was included then removed and has not returned. We were able to eventually work around this by creating a temporary line item with a negative $ amount that would adjust the total amount due shown. The line item could then be deleted after the initial payment was made this adjusting the invoice to the final amount due.  
The +/- feature has now been removed on the latest update and we have no solution to present a deposit or partial payment request. One or the other needs to return.