It will never happen, but this is how I'd do it:
Playoff championship for each level. Playoff results and relegation games involving the two lowest ranked teams in each particular division could be used for promotion and relegation. Promotion and relegation would largely stay regional, meaning that a team from the Premier West division would switch places with a team from the Champions West division, and so forth.
7 divisional games, 4 cross-division games, and 1 game against lower/higher conference.
Based on history, resources, existing affiliations, etc., I'd start like this:
PREMIER Conference
SOUTH Division
- Alabama
- Georgia
- Florida
- Tennessee
- Auburn
- LSU
- Texas A&M
- South Carolina
EAST Division
- Florida State
- Clemson
- Notre Dame
- Virginia Tech
- Miami
- Georgia Tech
- Pitt
- West Virginia
NORTH Division
- Michigan
- Ohio State
- Penn State
- Wisconsin
- Nebraska
- Iowa
- Michigan State
- Northwestern
WEST Division
- USC
- UCLA
- Stanford
- Cal
- Oregon
- Washington
- Texas
- Oklahoma
8-team playoff, including division winners and 4 wild cards, utilizing the Rose, Sugar, Orange, and Cotton Bowls.
CHAMPIONS Conference
SOUTH
- Arkansas
- Ole Miss
- Mississippi State
- Vanderbilt
- Kentucky
- Missouri
- TCU
- Kansas State
EAST
- Duke
- North Carolina
- NC State
- Wake Forest
- Virginia
- Louisville
- Boston College
- Syracuse
NORTH
- Indiana
- Purdue
- Illinois
- Maryland
- Rutgers
- Minnesota
- Iowa Sate
- Kansas
WEST
- Arizona
- Arizona State
- Utah
- Colorado
- BYU
- Texas Tech
- Oklahoma State
- Houston
8-team playoff, including division winners and 4 wild cards, utilizing the Holiday, Texas, Music City, and Camping World Bowls.
NATIONAL CONFERENCE
SOUTH
- Baylor
- Memphis
- SMU
- Tulane
- Rice
- Tulsa
- Louisiana Tech
- North Texas
EAST
- Cincinnati
- UCF
- USF
- ECU
- Marshall
- Southern Miss
- UAB
- Appalachian State
NORTH
- Navy
- Army
- Temple
- UConn
- Buffalo
- Ohio
- Northern Illinois
- Toledo
WEST
- Oregon State
- Washington State
- Boise State
- Colorado State
- San Diego State
- Air Force
- Fresno State
- UNLV
8-team playoff, including division winners and 4 wild cards, utilizing the Armed Forces, Military, Los Angeles, and Gasparilla Bowls.
REGIONAL CONFERENCE
SOUTH
- UTSA
- Texas State
- Arkansas State
- Louisiana
- UL Monroe
- Troy
- South Alabama
- Middle Tennessee
- Western Kentucky
EAST
- Florida Atlantic
- Florida International
- Georgia Southern
- Georgia State
- Coastal Carolina
- Liberty
- Old Dominion
- Charlotte
NORTH
- Akron
- Bowling Green
- Kent State
- Ball State
- Western Michigan
- Central Michigan
- Eastern Michigan
- Miami (Ohio)
- UMass
WEST
- Nevada
- Hawaii
- Wyoming
- New Mexico
- New Mexico State
- UTEP
- Utah State
- San Jose State
8-team playoff, including division winners and 4 wild cards, utilizing the New Orleans, Boca Raton, Arizona, and Frisco Bowls.