The situation varies. I'm going to assume you're in a wheelchair full-time; if you have some ability to walk short distances with assistance, you have extra options.
You can get from the station entrance to the platform, and then on and off the train, in a wheelchair at most stations. There is a short list of exceptions where you just can't get on or off the train.
These are the can't-travel stations:
Ashland VA
Clifton Forge VA
Coatseville PA
Elizabethtown PA (temporary problem which has lasted months)
Elko NV
Glenwood Springs CO
Harpers Ferry WV
Marshall TX (temporary problem which has lasted months)
Mount Joy PA
Newark DE
Paoli PA (this *might* have been fixed near the end of 2018, but check)
Parkesburg PA
North Philadelphia, PA
Westerly RI
At many stations, you will need to be lifted on or off using a portable wheelchair lift by Amtrak staff; a slow process. At better stations, you can roll on or off using a "bridgeplate". If you have specific stations in mind we can get you more information.
On most of the "single-level" trains (using Viewliner & Amfleet equipment), the sleeping cars each have one accessible bedroom with its own bathroom. The coach cars have a bathroom useable for some people in wheelchairs, but the car design is from the 1970s, so it does not really meet current standards for independent transfer.
On the cross-country "bilevel" trains (using Superliner equipment), the sleeping cars again each have one accessible bedroom with its own bathroom on the lower level. The coaches have a lower level which is wheelchair accessible, and I don't think it has a wheelchair accressible bathroom at all, but I'm not remembering clearly; I don't take long-distance bilevel coach very often.
On the California bilevel trains (using "California car" and "Surfliner" equipment) the lower level has a modern accessible bathroom.
On the Acelas (single-level using "Acela" equpiment) there is a modern accessible bathroom.
Staff are required to bring food to you (from the cafe, or the dining car if there is one) if you're in a wheelchair; they don't expect you to roll between cars, and in the bilevel trains, you actually can't; you're on the lower level and the connection between cars is on the upper level.