If you do an e-mail draft, it will be your best bet. Users can just log on and go to the players section and draft their players that way. You can stop it for a while and then pick it back up on Monday when the rookies will be entered after the NFL Draft. If you want to run two live drafts, it's a bit more complicated with some workarounds, but you can do it if you wish.
I think your best bet is to just run that e-mail draft though.