The first thing that would have to happen is all teams that wish to participate in the playoff MUST be in a two division super conference. To that there is NO Exception. Yes that means you too Notre Dame. In order to be in the playoff you must win your division. It would be up to each conference to settle it's ties. What this would do other than distinguish legitimate playoff representatives is allow big time programs to play each other out of conference each year without the result costing them a potential playoff spot. We would have Championship Weekend starting on Thursday night and settle all Conference Champions over that weekend. Thus the 1st round of the playoff.
The 2nd round would be held the next week using as many bowls as needed. For example we'd pair the SEC Champion and Big 12 Champion each year in the Sugar Bowl. Pair the Pac 10 v Big 10 in the Rose Bowl. In the Orange Bowl we'd probably put the Big East v ACC. and so forth. What this does is regionalize the 2nd round, uses the old BCS bowls and creates new season end rivalries. One of the things the BCS destroyed in college football was SEC goes to the Sugar, Big 12 goes to the Orange. This system puts new season end rivalries back into place.
The 3rd round, and this would depend upon the number of conferences we end up with. 8 would be ideal so I'm going with that. The 3rd round would have 4 teams left. These two games would be played at neutral sites each year possibly letting cities bid on them and the Championship games each year. Then the Championship Game would be held the following weekend.
Any team that failed to win their respective division and had at least 6 wins, would be eligible for one of the other 32 bowl games. These games would be played in the weeknights leading up to the playoff games on the weekend.
8 Super conferences with Division Champions would put 16 teams in the playoff.
2nd Round is held using as many of the BCS Bowls as needed
3rd and final rounds held on biddable neutral sites to be selected in advance. Everyone else gets to go to a bowl including conference championship runner ups.