Create a type N part number called Prepaid Deposit (or whatever you want).  Give it an Item Class that posts Sales to the Customer Deposit Liability account.
 
Add 2 lines to the Sales order in addition to the actual product line.  One for a positive quantity of Prepaid Deposit and one for a negative so the Sales Order still shows the original total because the Deposit lines cancel each other out.
 
Release the positive deposit line ONLY and print an dpost an invoice.  Receive payment from the customer as usual.
 
When the actual product is ready to ship, release both the product line(s) and the negative deposit line resulting in a correct invoice for the net amount due.

The AR-N Enter Customer Deposits program works fine linking a deposit to a Sales Order and printing an invoice reflecting the deposit received, and can avoid all this effort UNLESS the customer wants an invoice for the deposit.  Then you have to go this route.

Our prepay customers almost always need an invoice with detail first.