This is easy as pie.
Look at NCAA basketball. Even with a 68 team field, there are still two other tournaments that draw teams.
College football can go to a 16 team tourney. Play the quarters at Christmas, the semis at New Years, and the final the first week in January. Basically, the way it is now.
The non-tourney teams can play their bowl games before the tourney, all though December up to Christmas. So you have a regular season, a bowl season and a tournament season.
And don't tell me that will make the bowls meaningless. Most of them are meaningless NOW!!!! The bowls are a reward for a winning season and a reward for the alumni. There are enough cities and sponsors that want to be part of college football to fund dozens of bowls.