Customer Deposits

What's the best way to handle customer deposits?  Today we enter a sales order line for the final product, enter a line for the deposit and enter a negative line for the deposit.  We manually update the status of the deposit line and process it through invoicing and sales update to record the AR.  When the finished product ships we manually update the status on the negative line for the deposit and process both lines through invoicing and sales update to bill the customer for the product less their initial deposit.  Is there a better way to do this so