What I've done with the conferences so far:
ACC:
Added - none
Lost - UNC, Clemson, FSU & Boston College
Big XII:
Added - Houston
Lost - aTm
Big East:
Added - UCF, TCU & Boston College
Lost - Rutgers
B1G Ten:
Added: Rutgers & Notre Dame
Lost: none
C-USA:
Added: none...yet
Lost: UCF & Houston
MAC:
Added: none
Lost: none...yet
MWC:
Added: none
Lost: TCU
Pac-12:
Added: none...yet
Lost: none
SEC:
Added: UNC, Clemson, FSU & aTm
Lost: none
Sun Belt:
Added: none
Lost: none
WAC:
Added: none
Lost: none
I added BC to the Big East to put the conference at an even number of 10 programs and they were once a member before moving to the ACC. I considered adding Miami, but, I decided not to since I felt it would leave the ACC too weak with only one anchor program in football (VT). With the RL addition of TCU next year and a possibility of UCF down the road, I added BC as a decent team for conference SOS. New Big East is pretty strong with USF, UCF, PITT, WVU, TCU and BC.
SEC obviously started this domino effect with the likely RL additions of aTm, Clemson, FSU and UNC.
Big XII added Houston due to location and it making sense geographically. Plus, the Cougar program is on the rise and they could make for a viable mid-tier team in that conference.
B1G Ten added Rutgers whom they have reportedly been "courting" the last few years and Notre Dame who has always been discussed as a possible fit for the conference. With the Big East losing Rutgers, it caused them to poach BC from the ACC.
13-team MAC conference has not been touched, but, I am considering adding Temple to the Big East conference. However, I'm not sure I am down with 11 teams in the Big East and I don't think I want to add a 12th.
MWC loses TCU a year early and is a 7-team conference. Only anchor program is Boise State. May "dissolve" MWC as best I can by adding BSU to Pac-12 and possible SDSU to Pac-12/14.
Also, under conference rules, I set the current Pac-12 championship game to the Rose Bowl and not the team with the best record.
Also, I turned protected rivalries on for SEC and Pac-12.
I also changed the AQ status. ACC now automatically qualifies for a BCS bowl. The ACC winner no longer gets bid for Orange Bowl automatically. Big East winner now AQs for Orange Bowl instead of open BCS slot.
EDIT: Went ahead and added BSU to Pac-12 North and SDSU to Pac-12 South. Thus, creating the Pac-14. I considered Fresno State or Hawaii for the Pac-12 South slot, but, decided on SDSU. Therefore, the MWC is now down to 5 teams and is, for all intents and purposes, dissolved. 5 programs, no solid anchor program, etc. Just don't see them being much of a factor at all in the game.