The lower compartments seat 12 people. You can not go "car to car" in the lower level, as the cars are not connected by passageways on the lower level. Therefore, the lower level offers more privacy, as people will not be "passing through" your car to get to the dining room, etc. To get to the bathroom from the lower level. you exit your car and the bathroom aisle is are right there. As far as the bathroom smell, there is a door that separates your car from the bathroom aisle.
The upper levels have no bathrooms, and are "pass through" type cars. The dining room is on the upper level. People going to the dining car may walk through your car to get to it. Same goes for the lounge. Upper level people must go down to the lower level to get to the bathrooms.
We have taken the auto train to Orlando six times. We always had a great time. Our last trip on the auto train was three years ago. Since then our kids entered their late teens and 20's, got "real jobs" and no longer have the luxury of four extra days for travel. So they discovered the joy of flying and the 75.00 nonstop flights from our area. We do miss it, though.
I hope you have a great time. Its a wonderful experience for the family!!