Here is how college football's major championship will be determined for the 14 seasons starting in 2014, per Yahoo:
A group of 12 college presidents passed a plan for college football to have a four-team playoff starting with the 2014 season. The BCS Presidential Oversight Committee emerged from a meeting at the Dupont Circle Hotel late Wednesday afternoon to announce they have adopted the playoff format that had been approved last week by the commissioners of the 11 BCS conferences. The first playoff will take place after the 2014 season. There will be four teams, and the semifinals will be rotated among six bowl games over the life of the contract, with the championship game put up for bid. A selection committee will rank the teams, based on factors including head-to-head matchups. Semifinals will be held on Dec. 31 and Jan. 1; the championship game will be played on the first Monday that is at least six days after the last semifinal.
Here is how it has been handled for the past 14 years, starting with the creation of the BCS in 1998, per Wiki:
The BCS relies on a combination of polls and computer selection methods to determine relative team rankings, and to narrow the field to two teams to play in the BCS National Championship Game held after the other college bowl games. The American Football Coaches Association is contractually bound to vote the winner of this game as the BCS National Champion and the contract signed by each conference requires them to recognize the winner of the BCS National Championship game as the official and only Champion. The BCS was created to end split championships and for the Champion to win the title on the field between the two teams selected by the BCS. In that regard it has failed, as the 2003 NCAA Division I-A football season ended with a split championship.
Neither is perfect, but it seems as though the top one is better.