Bill Pay Option

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.

I'm afraid it isn't on our site now. I need for the customer to come to our site, add their account number, payment info and payment amount that will be interfaced with authorize.net then once payment is received we would then credit the customer's account in our own system.

You could have a product called payment, with a product option of the account number...then that could possibly fullfill your needs? Make the product option required and allow the user to type the account number in, at least that way you can have some visibility on that association. Would that work at all for you? It's not ideal, but it could get you mostly there. Also, maybe you could assign the type to the donation type, and allow them to set the price as well...