BCS is a strange way to pick the best. thumbs up to LSU! I went to Florida so am partial to Southeastern conference. i think you have to go for the two best even though they have already played each other.
LSU v. Alabama

What happens if Alabama wins? do they go 2 out of 3?

Actually there is a precedent for the winner of the rematch being named national champion even though they got beat by the same team in the regular season.
In 1996 FSU beat the top rated gators in the regular season finale. Then due to an odd series of other contenders losing the gators got a rematch with the Seminoles.
Since I'm not a gator fan & I am a Seminole fan I don't like to elaborate on the result of that game but the gators won the mythical national championship that year.
I have a feeling the LSU fans will feel the same way if Alabama prevails in a rematch.
They won't be playing 2 out of 3.

I wish college ball would get a playoff system in place. Until then we are stuck with the weird BCS system that we now have. It's better than no system but not much.
BTW, I don't consider the 9-6 LSU win as totally legit. I don't like the convoluted "overtime" that college ball uses. It's like penalty shots in NHL hockey. WTF??
As far as I'm concerned the LSU-Alabama game was a 6-6 tie.