modify cart process

We have an ecommerce system which needs a modification - this is NOT osCommerce, XCart, Magento or any other standard ecommerce system. We need to add in a field at checkout which will allow a user to enter an affiliate ID to assign that purchase to an affiliate - presently the user can access via a URL but we want to limit them to manually entering the affiliate ID in the cart. More details and link will be supplied to those showing ability in this - we would prefer to work with providers we have worked with before