We only offer the option to leave the playoff structure and bracket as is without re-seeding, or you can select to re-seed before the playoffs or during the first round and it will always put the best seed vs. the worst advancing seed. There's no direct way right now to totally make it a path to the Super Bowl through division only.
Also, in case you were not sure, you have 100% control of who makes the playoffs. You'll go to Commish Options-> Edit Playoff Seeds after the regular fantasy season ends.