TR,
Well having a deluxe bedroom will make you more comfortable and probably make the trip more enjoyable for you, it won't however make the booking process any easier. :lol:
Now seriously though, as Amfleet mentioned the deluxe room is quite nice and it is the largest room available on a train. You would indeed be traveling on the Three Rivers to Chicago, any other train would force you to backtrack to the east first before heading west to Chicago.
Now while you won't have a dining car on this train, your meals are still free in the lounge car, just show your ticket stubs to the attendent.
It's customary to tip the sleeping car attendant's, most people usually give around 5 bucks a night. If your attendent realy goes out of his way for you, then you may wish to give more. Also when you are on the Empire Builder, don't forget to tip the dining car attendent either. Most people leave a buck per person for breakfast & lunch, with 2 bucks per person for dinner.
If you find yourself having too much trouble with the Amtrak reservation site, you can always call 1-800-872-7245 to speak with a real person. Regardless of how you make your reservation, if you make it before the 15th of February, you can take advantage of a sale that Amtrak is currently running. You didn't mention if you are traveling solo or with another person.
Therefore I'll give you the codes for both of the sales. If you are traveling solo, then use code H259 which will get you 25% off the railfare portion of your ticket. There is no discount on the actual bedroom. If you are traveling with a companion, then use H255. That will get you the second ticket for your companion for free. If you do book on-line you enter the above codes in a box titled "Promotion Code" at the bottom of the page, after you've picked which trains you want to travel on.
I hope that this helps to get you started at least, don't hesitate to come back should you have more questions. I'll also add a few more things either later tonight or on Monday when I have a few more minutes.