Sounds like what you would need is the ability for a user to pay for their order, or create a new order and make a payment on that order(full or partial). Are orders placed/tracked on the site now? Seems like the best option would be to make sure that an order is created, and then allow some kind of partial payment on the order. Then subtract that partial payment and update the balance. Also, allow the user to type in the amount that they want to post for their payment. This way the user can post payments as large or small as they want. I don't think there is a way of doing this in the system as it is, you will need to do some customization. If the orders are already placed in the system, then it will be a bit easier, otherwise, you will need to automatically create those orders and add the items to it.