If it were me, this is the way i would have the conferences set up. Of course i would change the names though.
ACC - Boston College, Clemson, Flordia State, Maryland, NC State, Duke, Georgia Tech, West Virgina, North Carolina, Virgina, Virgina Tech
Big 12 - Missouri, Kansas, Kansas State, Baylor, Oklahoma, Oklahoma State, Texas, Texas Tech, Texas A&M, TCU
Big East - Cincinatti, UConn, Louisville, Pitt, Rutgers, Syracuse, USF, Notre Dame, Wake Forest
Big Ten - Illinois, Indiana, Iowa, Iowa State, Nebraska, Wisconsin, Michigan, Michigan State, Minnesota, Northwestern, Penn, Ohio State
Independents - Navy, Army, Air Force
Mountain West - BYU, Colorado, Colorado State, New Mexico, New Mexico State, UNLV, Nevada, Utah, Utah State, Wyoming, Boise State, Idaho
Pac 10 - Arizona, Arizona State, Cal, UCLA, USC, Hawaii, Oregon, Oregon State, Washington, Washington State, Stanford
SEC - Florida, Georgia, Kentucky, Tenn, Miami, Alabama, Arkansas, Auburn, LSU, Ole Miss, Miss State, South Carolina
WAC - Fresno State, LTU, San Jose State, Vanderbilt, Purdue, San Diego State