I think of Alinea as having 4 seating areas, although it's really just an upstairs and a downstairs. I don't really think of any of them being better or worse than the others (although I'm generally not picky about where I'm seated).
The downstairs room (on the ground floor) is just to the left of the entrance. The main advantage to this room is that you get to watch people's reactions as the enter the restaurant.
I think of the upstairs as having 3 areas. As you walk up the stairs you can go off to the right for one area. I would think that people consider this to be the most desirable spot since you're not really in a traffic pattern for any other part of the restaurant. If you go to the left from the stairs you will go through one area with seating on your way to the final room (the 4th area). Some people may consider this to be less desirable as people will walk through this room to go to the restrooms.
I've eaten in all parts of the restaurant and location really hasn't made a difference to me, but YMMV.
Also, jackets are a must. I've never seen anyone there in jeans with a jacket (although I know one person who has done that, but he wears jeans to every restaurant). My typical Alinea attire is suit with no tie.