I went with the real-world realignment through 2015:
http://www.cbssports.com/collegefoot...tball/21057704
Then after that it gets a little hairy. I forget exactly when I moved everyone, but I'll outline my thought process.
I haven't touched the SEC, B1G, or Pac-12, yet, outside of the real world changes.
I'm using UMass as my dynasty team, so as soon as they were good enough I moved them to the American. The MAC was already unbalanced, so this brings them back to a nice even 12 schools.
BC has been awful in the ACC so along with my move of UMass to the American, I moved BC there, giving me two rivalry games every year.
I personally can't stand having Independents, or competitive conferences without championship games (12-0 Notre Dame/Texas/some American team in the BCS Championship over a 12-1 SEC/Pac-12/B1G conference champ? No thanks.), so I've moved all the indies, and currently have Old Dominion as the sole team. With Navy's real life move to the American, it only seemed fitting to also put Army there. Air Force and BYU to MWC seemed like a no-brainer, and I sent Idaho along too since being in the Sun Belt didn't make much sense.
Notre Dame went to the ACC, obviously, and WVU was so out of place in the Big XII and too good for the American that I also moved them to the ACC.
I wanted to bring the American back to being an east coast conference, and bring the Big XII back to a championship division, so I moved SMU and Houston to the Big XII. So now I've got the Big XII as North and South divisions, with the South being all Texas teams.
I decided to go with a North vs. South theme for the American, and Tulsa seemed out of place, so they went to the Big XII to replace WVU. This makes the Big XII basically Texas vs. Tornado Alley. Cincinnati seemed good enough and didn't fit the theme, so they went to the ACC. Some traditionalists may hate this, but Duke and Wake Forest got "demoted" to the American to bring the ACC down to 14, to keep the North/South thing going, to give ECU some more rivalry games, to keep the American at 12 teams, and because it seemed a better competitive balance. At some point I moved Memphis back to C-USA because they just weren't good enough.
C-USA and the Sun Belt have been in flux a bit, still trying to find the right pieces to balance things out. At one point the Sun Belt only had 7 teams, and I found most of them were playing two FCS schools a year, so I made sure to move a couple C-USA teams to the Sun Belt. With 9 teams, they all get their 8 conference games and I haven't seen any doubling up in FCS games.
The last two seasons I've had Boise State and SDSU dominating MWC and the rankings (SDSU got torched in the BCS CG in my previous season, but somehow still led the Coaches & AP Polls, wtf), despite their only ranked games coming against each other in the MWC title game. For that reason, I'm moving both of them to the Pac-12 next season. I was considering swapping them for underperforming Pac-12 teams (likely Colorado and Utah), but I decided to go with the "Pac-14" instead, giving my all my "top-tier" conferences 14 teams, and the rest 12 or fewer.
I'm not going by any hard relegation rules, but I've got a rough outline for promotion/demotion to keep things balanced and geographically reasonable. As it stands now, I'm considering the SEC, Pac-12, ACC, and B1G as the top-tier conferences. The Big XII has been a half step behind them with the American right on its heels, then C-USA, MWC, Sun Belt, and MAC as the real bottom dwellers (Sun Belt and MAC, especially).
If I see a top-tier conference team having consistently bad years (both looking at record and <85 rating), they could get relegated down a step, but only if there's an available team that's has at least >90 OVR, a good record, and geographically makes sense. If I continue improving UMass, that means Syracuse is probably getting sent to the American soon.
At the end of each season, I've been entering records, rankings, and ratings into an Excel sheet and using that to make realignment decisions, and bowl bids for the next season. I've kept the Pac-12 & B1G getting the Rose Bowl, ACC gets the Orange bowl, and the SEC the Sugar Bowl. Depending on the average ranking of the conferences, and how many top 50 teams they have, the American or Big XII either get the Fiesta or at-large bids. I also gave the MWC an at-large bid for my current season based on their performance, but I doubt they'll keep it once I move Boise & SDSU.
Here's my current conference alignment, with Boise & SDSU soon to be on the move. I also want to move Tulane out of the American, party because they're terrible and partly because an empty Superdome is just depressing to play in, but I haven't decided who to replace them with yet. Leading candidates are MTSU or Southern Miss, or a two team move bringing FAU & FIU up and sending ECU down with Tulane.