My thoughts, Doesn't mean its bad or wrong just not my liking...
First of all, get rid the of Conferences. Unless you are running at least 18 teams you don't need them. Go to three divisions, 4 teams per division. That enables you to have a 14 week schedule - Every team plays inter-division twice and everyone else once.
Second, in a 12 team league you have way too many teams making the post season. We run 12 teams and only have 4 in the Big Championship Bracket (for the big money). Division Champions (3), plus the team with the highest record (make sure you have good tie breakers, ie. h2h, points for, points against, etc.). That way your playoffs extend only until to week 16. Week 17 benches have no implications on the big game.
Third, some might disagree with me here but from my experience playoffs don't work in the fantasy football settings. If you want to get more teams involve in the post season go to a bowl system (that's what we use). You still have the Championship game as explained above and then you can add a "Toilet Bowl" for teams seeded 5-8. You want to get everyone involve add a "Losers Bowl" for teams seeded 9-12.
Good luck and free to pm with any questions.
Best Damn Fantasy Football League