It shouldn't matter, since you should be spending the majority of the trip in the Sightseer Lounge car!

Definitely pick the upper level--you'll be able to see much more of the scenery, since you'll be above the level of most of the trees and buildings along the track. (That said, seriously, for the ride through the Colorado Rockies, even the upstairs doesn't do it justice--you MUST ride that portion of the route in the Sightseer Lounge, which has curved glass windows into the ceiling that allow you to look up at the mountains towering above you.)

The only advantages the lower level has is a cozier, quieter atmosphere (there are 12 seats in a smallish compartment off of the main vestibule area) and easier access to the restrooms and doors to the outside (as they're all on the lower level). Otherwise, the upstairs is far more convenient for moving throughout the train (since the doors connecting the cars are on the upper level), and the stairs aren't that difficult to navigate for the occasional bathroom trip. I've never had a problem with the upstairs being too noisy--especially at night, everyone seems to fall soundly asleep and the loudest noise is the air conditioning in the car. (However, sometimes you do get screaming kids or cell phone yakkers...)

There should not be a price difference between the two. It looks like the lower-level coach is an add-on to the railfare, but it should actually come out to the same price as the normal upstairs booking.