I haven't exactly done a bill pay but I have been using a free service for an online shopping cart that is really easy to use. It can be set up to take either credit cards or paypal and it is easy to integrate. Basically you would just add a pay your bill button and a link that they provide. It is processed on their secure server and the info goes into a secure database. They send you an email when you have a purchase or payment and you log in with your password and retrieve the credit card or paypal info and process the payment manually.
Mine have always been a fixed amount but I am sure you could set it up where they entered the amount they want to pay and check out.
If you want to take a look at it you can find it at www.mals-e.com