They will never get rid of the Minor Bowls, they bring in extra Revenue for Teams and those Hosting. SO, don't get rid of them.
Each Conference Champion would go into the Play Offs, which would be housed at the greatest of the Stadiums (Sugar, Rose, etc. Pretty much your BCS Bowls). You don't win your Conference you got no right to cry about not being handed a chance at the National Title.
The 2nd in Conference would get an Automatic Bid to the 2nd Tier (non-Playoff) Bowls to go get more exposure and money, being pitted against another Conference Runner Up. After that you do your Bidding System, with 6+ Win Teams qualifying.
The good teams get extra games to gain more Revenue and expose their Seniors before the NFL Draft comes along. The Runner Up not only gets the money from playing in the Conference Championship Game (for Conferences that have them, and I think every Conference SHOULD) but is getting another Nationally Televised game against another 2nd In Conference Team for even more exposure and Money in a 2nd Tier type of Bowl Stadium (Cotton, etc).
The rest of the bunch gets to have one last swing as well, just like now.
You don't hurt anyone because you keep all the Bowls so that so many teams get what they get now, more money and exposure. You reward 2nd in Conference by giving them the better Stadiums than the rest of the pack and give them a decent team to face in another Runner Up. You REALLY hook up the two teams that make it to the Final, as they get another 2-3-4 games of Revenue and Exposure in the Best Stadiums in the Land. You give the Fans a Last Man Standing Champion.
Sounds easy enough to me.