Invoice Payment Implentation

Looking to put some implementation into a site whereby a user can enter a reference number of an invoice and the amount they wish to pay using Woocommerce. The invoices don’t need to be stored on the system in any way. It’s just a case of allowing the user to make a very simple payment without actually purchasing a product.

Has anyone had to implement something along these lines or have any thoughts on how I could do this?

http://wordpress.org/extend/plugins/woocommerce/