You can edit the roster of your created team, yes (except I didn't see player equipment editing, though I may have missed it). You can base your roster off of any in-game FBS team (though judging by Virginia's template, they aren't nearly 100% correct), but I didn't see any FCS teams in the roster template list.
My only complaint with TeamBuilder is that there aren't enough number fonts, particularly compared to other games with robust create-a-team interfaces (Blitz: The League, All-Pro Football 2K8). Hopefully more get added in a future iteration of TeamBuilder. Other than that, great job EA!