To answer the original question:
The top eight teams are seeded based on merit. Once the seeds are determined they are placed into the bracket according to the following guidelines:
All pairings will be made by the NCAA Division I Football Championship Committee. The following principles are applied when pairing teams:
1. The teams awarded the top eight seeds shall receive a bye in the first round and are placed in the appropriate positions in the bracket (Nos. 1, 8, 4 and 5 in the upper half; and Nos. 2, 7, 3 and 6 in the lower half);
2. The remaining 16 teams will play first-round games and will be paired according to geographic proximity and then placed in the bracket according to geographic proximity of the top eight seeds previously placed in the bracket
Therefore, as long as the committee follows their own rules and seeds the teams first, there is no way that SEEDED teams will be placed into a certain part of the bracket based on their geography to other teams in the bracket. The rules clearly state that the teams seeded 1, 4, 5 and 8 go in the upper half and teams seeded 2, 3, 6 and 7 go in the bottom half.
Now, as has been stated previously once the seeded teams are placed then yes the other teams are placed based on their geographical proximity to each other (for first round games) and to the seeded teams (for second round and beyond).