On Superliners, I prefer the upper level, just behind the stairs. You miss out on getting a tray table, but the extra 2-3 inches of legroom makes it just the right amount of space for me to stretch out fully. I am 6'3" and in the regular Superliner seats, I can't utilize the foot rest and calf rest at the same time. It may be a little brighter/noisier than other places in the car, but it is the only seat that I can FULLY stretch out in. If you bring earplugs and a hat to shade your eyes when sleeping, it works out well.
As for the lower level, Caravanman is on the right track... Generally, those with disabilities are given priority for lower level seats, but there is nothing preventing a non-disabled individual from reserving a lower level seat. Case in point, on my trip last week the upper level seats were all sold out, so I ended up on the lower level on the SWC from CHI to KCY.
Edit: Added comments on Lower Level seating