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.