Security :: Windows Authentication - Get Role Security In Web Config File To Coincide With Controls

We use Sharepoint to control our websites. We build the sites, then load them into the sharepoint server. My question is if I use windows authentication, how can I get my role security in my web config file to coencide with the asp.net controls that use the Forms authentication. Is there a differenence? Our security uses a session variable for security but there is no where to set up their permissions except in active directory. I hope this makes sense because I would like to implement the LoginView with Role groups but how can I give them the role="administrator"? Do I have to go into active directory and give them these permissions(would take awhile due to the size of the company)? Or do I have to set up priveladges in the web.config file for each user(difficult I think)?