Ok, I'm still getting questions, so here's some clarification:

Each player must control a character. The player must also control a faction during battle, of which their character may be either the leader, or just a regular old member. For example, if you're playing a run of the mill member of the Green Ajah, you will dictate what your entire Ajah is doing during battle (the members that are present, at least). 

I'll add this information into the introductory post.