We have done the Auto train twice and both times requested the lower level. It is the same price as the upper level.
The lower level is basically a room with about 16-18 seats. Since it has only one door into it you will not have people walking the aisles to go to the bathroom or whatever during the night, like you do on the upper level. It is much more private on the lower because of that.
Both times we were on the Lower Level, we were there by ourselves.