I've heard that meals are being brought to your room, so no social mixing in the diner.
On the AT, roomettes and the family bedroom don't have private baths, so one would have to use the shared toilets. Everyone should be wearing a mask when outside of their room; passing in the hallway, while close, would be brief. COVID transmissibilty via surface contact (as in the bathrooms) is said to be much less of a concern than face-to-face.
Standard bedrooms have an en-suite private bath. They're really designed to sleep 2 in upper and lower bunks, but a 3rd person can squeeze into the wider lower bunk if you don't mind crowding together. Some bedrooms can be connected into a 2-room suite, but that could get expensive for 3 people. Another option would be to get 1 bedroom and 1 roomette in the same car for sleeping, and share the bedroom's bath. (If you want a single bedroom for 3 people, you may need to make reservations by phone or at a staffed station rather than online.) Here are the bunk dimensions for the bedroom:
https://www.amtrak.com/superliner-bedroom