I've played in a league with divisions (although not on yahoo). I think you just play the people in your division twice and everybody else once. and the top of the division makes the playoffs as opposed to just the top 4 teams overall.
I play in divisions annually. Its difficult for the schedule and bye weeks. It also depends on when you start playoffs and how many teams make the playoffs. We do 6 with the 2 division winners getting a bye week and the other 4 play in first round. We usually start playoffs in week 13 so last week of season is not used since many playoff bound teams bench stars in last game and its not fair to us fantasy players