Notre Dame shouldn't figure into the BCS as an at-large. If the Golden Domers are in the top8 they are in. Even if they're picked as an "at-large" it doesn't count against the non-AQ conferences. They are essentially considered a member of an AQ league for these purposes, and their selection doesn't impact the chance that OHIO (or any other non-AQ team) gets called (unless we're in the unlikely situation that two non-AQ conference champions are in the top12, in which case only the higher ranked is guaranteed a spot, and the other team would be a true at-large)
It most certainly "counts" against non-AQ schools. Notre Dame is taking away another potential spot of an at-large. Notre Dame isn't affiliated with a conference, so technically their bid will be an at-large bid. Judging from recent history we'll most likely get two SEC, two Big Ten, two Big XII, one Pac-12, one Big East, one ACC and one at large. If this season holds true, that means the Irish are getting in.
We are going to need A LOT of help in this scenario. I personally don't think Notre Dame will make it to the BCS given their schedule and can also see two PAC-12s and two ACCs that are more deserving. We'll see how it shakes out. Go unbeaten first and then we'll talk.
The "ranked in the Top 12" thing is kind of misleading because there are only 10 spots for BCS games.
BY RULE, a top12 conference champion from a non-AQ conference (the top rated one if there is more than 1, NOT COUNTING notre dame) WILL be included in a BCS game. There are only 6/7 automatic qualifying teams: the champions of the ACC, Big East, Big 10, Big 12, Pac 12, and the SEC, as well as Notre Dame should they be ranked in the top 8. Those spots, plus the highest ranking non-AQ team are automatically in, they are not really at-large selections. The ONLY POSSIBLE WAY notre dame affects a non-AQ team's chances is if
(1) there are 2 or more non-AQ-non-Notre-Dame schools ranked in the top12
OR there are 2 or more non-AQ-non-Notre-Dame schools ranked in the top16 and one AQ-conference champion is ranked lower than both of them,
and (2) Notre Dame is ranked in the top 8 (they might also need to have 9 wins, can't really remember, but they're not going to get one without getting the other).
The "ranked in the Top12" thing is not misleading. There are 10 spots and no more than 7 automatically qualifying teams (counting a #8 notre dame as an AQ team). While it is theoretically possible that #11 Boise State and #12 OHIO both get into the BCS (just picking 2 random examples), it wouldn't happen. OHIO is NOT getting picked as an at-large if there is a higher ranked non-AQ conference champion. Heck, just last year
#8 Boise State (who were not the MWC champion) went to the MAACO Las Vegas Bowl instead of being an at-large selection for the BCS. And that was with the winningest QB in NCAA history and having preformed superbly (and traveled well) on the BCS stage in the past. Notre Dame, who to reiterate doesn't satisify the requirement that the BCS take the highest ranked non-AQ team that is in the top12 or top16 and ranked higher than an AQ champion, making or not making the BCS has no material impact on the chances of OHIO playing in the BCS this season unless we are the highest ranked non-AQ conference championship and in the top12 (or 16). Sorry for the repetition.