Go to the station and find out from the staff there.
Different train routes can have different procedures.
Last time I rode Amtrak was nine years ago and I am sure it has changed, so I won't go into details that might no longer apply.
Originally Posted by
adventurepdx
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Here's a photo when I took the Capitol Corridor between Sacramento and Berkeley. The bike hook area is similar to what you'll find on the Surfliner:

If the procedure is to use hooks in an area like that, you might be able to hang it from a rear wheel and pull the front wheel off the bike if the bike is too long to fit. Then strap the wheel to the bike so it does not get lost or damaged. Leave your water bottles empty so they do not leak or fall out from the weight.
The 50 pounds likely is for the bike without your luggage. Amtrak has generous carry on criteria for all your luggage, much more generous than an airline.
There was an Amtrak employee at the nearest station to my home that would not let you strap two panniers together to call them one item, so I ended up buying a light weight mesh duffel that met their size criteria that I could put a lot of my stuff into, that mesh duffle weighed almost nothing and sat in the bottom of a pannier for my Pacific Coast trip. Photo below was my carry on luggage for my Amtrak trip home from that Pacific Coast trip. On that trip, I also had another duffle that I used for checked baggage, that is not in the photo.