Applying Deposit to an AR Invoice

 1.        Create an AR transaction type for Advance Invoice with class Deposit 
 2.        Using this transaction type, create a Deposit for the same customer 
 3.        After receiving the amount from customer against this Deposit Invoice, create a Receipt 
 4.        Apply the receipt with the Deposit 
 5.        Now Create the required Sales order for the customer and ship confirm 
 6.        This will create the end customer invoice with full amount 
 7.        Now query the end customer invoice and apply deposit(Action–> Apply Deposit) by querying the deposit which created earlier 
 8.        Save the transaction and then click the refresh button in the Balance Due block, you can now see the difference amount after Deposit deduction 
 9.        Also you can see all adjustments in the Details button

Note: Final Invoice date should fall in between Deposit Invoice effective dates