Hmm. First of all, no problem keeping the berth down all day. Just keep reminding the attendant, as they go through the car on autopilot making up rooms when they see the chance. If you tell them when you board, and they forget, they should have no problem undoing it, it only takes a few minutes.
On the other hand, all Amtrak trains can get moderately bumpy at times, even often. People say the center is better but I wouldn't panic about that, I've found that all bedrooms can get rocky. It is actually rare that the ride is completely smooth, usually it is the equivalent of light turbulence on a plane, with the occasional jolt. Let's say that in the dining car, I wouldn't want my coffee cup filled to the brim, but I don't think I've ever seen one actually fall over.
I can't estimate how much the slight bumpiness will affect your pain, you might want to get some better advice from your doctor. Will you have some pain meds?