My experience is mainly on been on the Coast Starlight, Cascade, Lake Shore Limited and the Empire Builder routes. None of those trains allow bikes in the passenger cars. Bikes are rolled up to the baggage car and loaded, but spots for the bikes need to be reserved when purchasing tickets.
Even on routes where bike still need to be boxed, it is easy, and minimal disassembly is required. Amtrak boxes are large, and only require pedal removal, and loosening the stem to swing the bars parallel to the front wheel. Then the bike is rolled into the box. Not a big deal. They sell the boxes for $20.
The Empire builder might fit your needs It goes from Chicago to Seattle, WA or Portland, OR. A couple of years ago we finished a tour in Detroit, MI, and we wanted to take the train home. My brother gave us a ride to Toledo, where we caught the Lake Shore to Chicago. From Chicago we took the Empire builder to Seattle. From Seattle we took the Cascade back to Oregon. The Empire builder splits Spokane, WA part going to Seattle, and part going to Portland. the bikes going to Portland need to be boxed, those going to Seattle are on the baggage car's bike hooks.
Where are you starting your train ride?
This is the Cascade in Seattle, WA. If all the bike hooks are used, the bikes need to be boxed. Our panniers are carried onto the train, and we have never had a problem doing this.
