I just rode the train down from Montana to Albany earlier this week. Albany is the stop north of Eugene. Our bikes were boxed. The unboxed bikes are hung from hooks in the baggage car. I am pretty sure that they will want the panniers off of the bike to get them on the hooks. Presently the trains have a car that will hold 6 bikes, but they are planning to upgrade to 12 bikes in the near future.

We could not get a reservation for unboxed bikes. But if we could have our plan was to use the lightweight duffel bags we use when we box our bikes (for any mode of travel). We empty the contents of our panniers into 2 large, very lightweight duffel bags, and leave the empty panniers on the bikes when they are boxed. That cuts down the amount of items we have to handle. We thought the empty panniers could have been hung up with the bikes.

We were transferring from the train to an Amtrak connector bus in Canada. My wife is standing by our luggage. The 6 empty panniers are in the bike boxes in the cargo bay of the bus. The contents of my 4 panniers fit in the large duffel bag, and my wife's 2 panniers into the black one. It is almost easier to box the bike for the train in some situations. Amtrak boxes are very large. It takes about 10-15 minutes to take the pedals off, pop the bars and stem loose , roll the bike into the box, and tape it shut.