Great info this is gold.If you call Amtrak to book (as opposed to booking online), you can choose a specific Roomette based on what is available. You should first join Amtrak Guest Rewards online (this allows you to get points for your trips), and after you have an account number, call the dedicated AGR number (1-800-307-5000) to make reservations. The AGR agents are often more knowledgeable, and should know how to select a particular room.
I like lower-level Roomettes (11, 12, 13 & 14) because there is less traffic in the hallway; and you are closer to three toilets, the shower, the luggage rack, and the door to go outside at fresh-air stops. Also, you can clean the outside of your window either in Chicago or at a fresh air stop (depending on whether or not your room is on the side of the platform).
It is not possible to predict on which side your room will be; the cars can be oriented either end forward.
I always print a copy of the schedule with mileage, as well as a route guide. Here's a link to the route guide:
https://juckins.net/amtrak_routes/route_guide_Empire_Builder.pdf
I would have thought upper cars had better views? Bathrooms are all on first floor then right?