A better way I think is to:
Create an Item to use on the paylink that credits a deposit account, not income.
Create a second item that Debits the deposit account and Credits inventory.
Add this item with the amount of the deposit to the sales order.
When sales order converts to invoice. AR is net of the deposit and customer deposits is reduced.
Also create a report for the customer deposit account that allows you to group the debits and credits for a sales order and set it to only show open balances.
