It's an experience, good or bad, depending on your companion's personal hygiene and personality. I've had some wonderful trips where I got to talking with my companion and we found out we had mutual interests, and they ended up as buds for the trip. I also had one trip where I was next to a guy who smelled like he'd bathed in aftershave lotion five minutes ago. My advice is to see how it works, but if things don't feel right, then talk to the conductor and see about moving.
As for luggage and stuff, you're in luck. There's a large luggage rack in the lower level of the coach where you can put suitcases. Above the seats is a large rack that will hold most carryons without any issue. I've never seen the top racks overfilled to the point there isn't room for more. Restrooms are in the lower level, and are private rooms (small but private - can get dressed, wash up, or address other needs in relative solitude).
Another thing is there is a lounge car, so if you start feeling claustrophobic in the coach, take a good book and wander to the lounge car. The top level is a mix with some table seating and individual seats / couches facing out.
My advice is to bring a good book(s), MP3 player, etc, so you can relax that way. Plus enjoy the scenery - the route you're taking is really neat looking. Amtrak has route guides on the trains which will tell you the highlights of the trip - if you don't have one by your seat, ask a train crewperson.
Hope you have a wonderful trip, just relax and don't be afraid to ask a crewmember if you have any questions.