Lower is better. But it depends on the show. I saw the Allman Bros there a few years ago and the lower was the place to be. Actually, there is not a bad seat in the house. An excellent venue for a show.
Lower Balcony is closer to the stage and has a better view. If you are in the first couple of rows there and in the middle the seats are OK. You can look at a seating chart here: http://www.beacontheatre.com/seating/Personally I don t think the sound is as good in the Balcony.The Upper Balcony are the least desiarable seats.