Ben,
Not to be a stickler, but on an automatic it's not a flywheel(as there is almost no weight), but rather a flexplate, and since we are talking about taking the trans out, the bolts it refers to go thru that flexplate into the torque converter, and unless yours is different than mine those two(the torque converter & flexplate) can actually line up in 4 different positions. Now as to if there is really any reason to line those two back up is more than a little questionable as they are neutral balanced seperatly from the factory...
Personally I question if getting the drive shaft/yoke back in the same position even matters, I've done it both ways & can't say I've seen or felt a difference