Suggestions on how to get eCart to handle both credit cards and invoices

I am trying to build a checkout system that mirrors a current one I built with a different system and a lot of elbow grease. Currently when a client is ready to check out I take them to a login page where they can either log in or sign in as a new user. A new user can sign up either as a consumer (where they are taken through a credit card payment option) or as a corporate user (where they are sent an invoice). The only real different between the two users is that there is a true/false flag set in a db table and whether the credit card info is captured. Although I have yet to be able to get the eCart checkout wizard to work for the credit card checkout, I was thinking once I did this that I could find some way to change the pages generated to meet my needs. Am I going about this the wrong way?