I haven't done this for football, but was in a league this past year with divisions for baseball. We had it setup in 3 divisions of 4, and the top 2 teams from each division made it to the playoffs. This was an ESPN league also - and our commissioner was able to set it up that way. I'm sorry I don't have any experience with it in football, but if we could do it in baseball, I am sure there is a way to do it in football.
If you still can't figure it out, I would try their help page - Click me!
. If the information is not there, go ahead and click the "Contact Us" link and directly ask them the question.