You can enter a positive invoice in 3-2, but invoice type memo so that it doesn't affect the billed against contract amount.  Down in the grid code it to a liability account called Job deposits.  Use the job # as the subaccount number.  This will debit AR and credit the liability so it shows on the Balance Sheet and not the income statement.

Then apply their payment in 3-3-1.  To show it as a payment, you will then enter a credit invoice in 3-2, also type 3=memo, and code it against the liability account to reduce the balance.  Then apply the credit towards other invoices in 3-3-1

Thank you so much for your reply! What module in sage is this done?

The menu numbers are in my response. This is Sage 100 Contractor? 
I don’t know Sage 300