If you do not have to issue an invoice for the downpayment, then you can input it into A/R through  
AR-N.  When you issue the final invoice, you will be asked whether you want to apply the deposit.  You can select any dollar amount from the customer deposit.  When you print the invoice, it shows the total original amount, then there is a line with the deposit, then the balance.  Looks real clean.  Try it in a test company.
 
I really like the way DBA handles these deposits.   Much less cumbersome than my other system!

Thank you very much!!  We do use Sales Orders and I just went in and linked the deposit to the SO...it works great!
 
Thank you both for your help!