It's going to be 12 episodes. The anime is announced to have total 6 DVD/BD and the last 6th DVD/BD have 11 and 12 episode.
As for the story arcs, each manga have story arcs. Sometimes it's more clear when a new story arc begins, sometimes it's not so clear. But Prison School definitely have story arcs and it really doesn't matter if the author have named them or not. Usually if they are named, that name is used, but when they are not named usually a fan-name is made usually after the item, location or event for which is about.