If your plan is to have the SSL and Dining Car accessible to your Mom, then you should definitely consider getting a room on the upper level.
That way, you just have to climb the stairs twice - once to get on and once to get off.
The SSL and Dining Car on the Superliners are only accessible through the upper level.
You cannot move between cars at all on the lower level.
If you get an upper level room, no matter what, once you're on the upper level, the most convenient bathroom will be the one near your room.
On Superliner trains, there are no bathroom(s) in the Dining Car, when available - there is one on the lower level of the SSL in the Cafe, and all coach bathrooms are on the lower level.
The only upper level bathrooms on the Superliners are in the sleeping cars.