On train #3, the Southwest Chief, you will be accommodated in a Superliner Coach. Superliners are bi-level cars which seating is located on both the upper and lower levels of the car. While you enter the train on the lower level you will access the rest of the train (Diner and Lounge cars) via the upper level.
“UL” stands for upper level seating and “LL” stands for lower level seating. The upper-level is the main seating area with about 60 seats, while the lower level holds only 12 seats. Half of the lower level is equipped with restrooms while the other half has an enclosed seating area intended for passengers with special needs (for instance elderly and those who need close access to restrooms or are unable to climb stairs to the upper level). I recommend the upper level seating for the better view and easy access to the rest of the train. The lower level is kind of grim and it’s a bit noisy since you are closer to the trucks (train wheels) and the rails.
There are 5 restrooms on the lower level; 3 restrooms are small airplane type facilities, 1 restroom is specially equipped for handicapped needs, and the other restroom has a vanity area as well as an enclosed toilet usually intended for female passengers only. The coach seats are extremely comfortable, much more from your standard airline or bus coach seat. The seats are large, plush, and recline way back. Each seat has an individual reading lamp, tray table, footrest, extendable leg/calf rest, and lots of legroom.
I have never or heard of any problems with people leaving laptops or CD players at their seat. However, don’t just leave them sitting around while visiting other parts of the train. Make sure the items are put in there proper cases and stowed in another suitcase or where not visible. Under the seat in front of you or in the overhead luggage rack is usually a safe place. If you are worried you can always bring these items with you to the lounge and just keep them by your side. Again, I never heard of any problems regarding this.
Now regarding train #41, the Three Rivers, which you will be taking to Chicago. This train is a single-level train meaning all coach seats and restroom facilities are on one level. The seating is set up as and has the same features as on a Superliner, but there are only two restrooms per car. Both are of a good size, one is specially equipped for handicap use. In fact I will be on this train next week, so you will be able to find more detail on this train in my trip report when I return. Best of luck with your trip and I hope everything works out.