Okay, I’m a little bit confused here. For some reason when the new BCS format was unveiled this year, the National Championship Game was added. Now, for some reason, I thought that this simply meant that the top 10 BCS-ranked teams would simply play in those five games. But now, I just realized that the BCS National Championship Game will be played after the four traditional bowl games between the #1 and #2 ranked teams that emerge. Is this actually correct? If so, then have we indeed taken the first baby steps towards implementing a true playoff system in college football? 
That’s incorrect - that’s the premise of the BCS+ idea that was floated a few years ago. That is, play the bowl games - then play the #1 and #2 AFTER that.
The way it will work this year is that the #1 and #2 at the end of the season will go to the NC game on Jan. 8th. The four other BCS bowls will fill in according to their picks/tie-ins/standings/etc.
More clarification…
The real change this season is that they’ve made the National Championship game stand alone, rather than making the National Championship rotate between the Fiesta, Sugar, Orange, and Rose bowls.
So this year, Arizona will first host the Fiesta Bowl, then a few days later, the National Championship Game.
Ah, okay. So then my original premise was correct. Basically, the top 10 ranked teams at the end of the season will play in one of the BCS Bowl Games (the four traditional games plus the National Championship Game). Thanks for the clarification!
I wonder where Rutgers will place if we finish 12-0… 
Well, not exactly. Here’s a good site if you’re interested in the particulars.
Basically, you don’t have to be in the top 10 to qualify. Granted most of the bowls will be filled with top 10 teams from the BCS standings, but it’s not guaranteed. Boise State, as a good example this year, can qualify if they stay in the top 12 in the rankings.
If Rutgers goes 12-0, they will be the Big East conference champions. That gives them an automatic berth. I doubt very much that they will be top 2 in the final standings, so they will go to one of the regular BCS bowls. I’ve heard the idea kicked around of an undefeated Rutgers v. an undefeated Boise State in the Fiesta Bowl. BUT…
Rutgers still has to beat West Virginia.
Boise State still has to beat Nevada (and they got all they could handle v. San Jose State).
So, we’ll see how it shakes out.
More broadly, the winner of a BCS conference gets an automatic bid. It’s conceivable that the, say, Big East next year could all beat each other up, a la the SEC and have no teams in the top 25 but the winner of their conference still gets a BCS bid.
A brilliant example of this is Pittsburgh in 2004. The Big East was in a state of disarray, and 8-3 Pitt ended up winning it. This qualified them automatically for the BCS. They went on to the Fiesta Bowl where they got embarrassed by Utah 35-7.
Pitt’s rank in the final BCS standings of 2004? 21st.
It seems that every year a team comes along that exposes a flaw in the BCS system. The BCS then makes a rule change to correct the flaw. The following year another team comes along that exposes a flaw, and on and on and on . . .
The resistance to a playoff gets more ridiculous each year. But, money rules!