OK, lets hit some basics, then.
On trains other than the Auto Train, everyone in coach is given a "seat check", which is a little slip of paper clipped over your seat that indicates where you're getting off of the train. This is important on those trains because everyone gets off at different stops and the conductors only work for a portion of the route. On the Auto Train, you don't need these because everyone is going to the same point. Instead, you're given a slip of paper that lets you know what time you're scheduled for dinner. The Auto Train is unique in that it has 2 dining cars, one for coach passengers and another for sleeping car passengers (and the meals are included for ALL passengers). On all of the other trains, there is only 1 dining car. Meals for passengers in sleeping cars are included, and passengers in coach are able to eat in the diner (but have to pay cash).
The "40/41" numbers come from the car numbers - from the thread that Alan linked, here is what the consist of the Auto Train looks like:
AUTO TRAIN — 2 sets
----|---- —— Superliner Dorm
5245|5345 —— Superliner Sleeper
5243|5343 —— Superliner Sleeper
5241|5341 —— Superliner Sleeper Deluxe
----|---- —— Superliner Auto Train Lounge
----|---- —— Superliner Diner
5240|5340 —— Superliner Sleeper Deluxe
5242|5342 —— Superliner Sleeper
5244|5344 —— Superliner Sleeper
5210|5310 —— Superliner Coach
5211|5311 —— Superliner Coach
5212|5312 —— Superliner Coach
5213|5313 —— Superliner Coach
----|---- —— Superliner Auto Train Lounge
----|---- —— Superliner Diner
----|---- —— Superliner Diner (as table car)
The first two digits of the car number refer to the train number 52 or 53, depending on what direction the train is going. The second two numbers (either 1x for coach or 4x for sleepers) refer to a particular car. When you call to get a room, you'll be assigned "Bedroom E in Car 5241" for example, which tells you exactly where on the train you're going to end up.
Does that help?
Edit for your second question - that's really the only difference. The point made about public restrooms if you're in a roomette is a good one. In the deluxe sleeper you have 4 public restrooms for 4 roomettes and the Family Bedroom. In the regular sleeper you have 5 public restrooms, but they're shared between 14 roomettes and the Family Bedroom.
Deluxe Sleeper:
"Normal" Sleeper: