Hmmm, neat concept.
Are you doing a manual draft? If so, just tell each team which division (conference) they're in, and they can only draft players from the conference. As the commish, you input the players, so the online system doens't really play a role. I guess the online draft is probably the same. However, I don't know of an online sytem that will do these things for you in an autodraft setup.
Does anybody else know of one?