My husband and I had a good experience with 2 bikes, taking Amtrak from Raleigh, NC to Tampa FL in Feb 2011.
We did learn some important things: A road bike larger than size 54 inside an airport-grade bike box exceeds the 50 lb limit. You can only put a bike box on/off at a train station with luggage service. You must arrive at Amtrak station at least 1 hour before departure if you are checking a bicycle.

We stuffed some rags and dirty laundry inside the cardboard bike boxes with our bikes. No damage to bikes.