So in addition to boxing your bike, you can also reserve a bike slot and when the train arrives walk your bike to the baggage car and hand it to an attendant.
There is also carry-on service, where you bring your own bike on yourself and put it in the designated area. I have twice taken my bike on the Vermonter that way. It has three cubbies/train. You hang the bike by the rear wheel. My LHT is large, so I have to remove the front wheel before hanging. There are no seat across from the cubbies so there is plenty of room to do that without getting in the way of passengers. The biggest pain is getting it into the coach. The vestibules are not spacious enough to allow you to maneuver the bike with panniers attached. I removed them on the platform and put them in a sleeping bag mesh storage bag that I didn't have any need for and carried them on that way. You could also use a thick trash bag.