You have to ride the train that accepts bicycles, otherwise, you have to box it (and it's treated like luggage). When you make your reservations, there's a button on the chosing-which-train-and-price page with the words "Review Upgrade Options". Click it, this takes you to a page with, of all things, upgrade options, which if available will have a bicycle option. Click it, it adds $5 to the cost of the ticket, and you can then wheel your bike as-is to the train and it will hang from the front tires.

I just did a test, and selected June 15th returning June 30th, SEA to PDX, 730am, and there was a bicycle option available. This means that this particular train/time has at least one space for a bicycle-not-boxed. I have no experience with xtracycles.

Also, tricky, is that you can't get off many destinations in-between Seattle and Portland, because they don't have anyone at the stations to unload the luggage. You can't do it yourself because the conductors won't open the luggage compartment doors. In case you were considering something like that.

I second the Lucky Lab and Deschutes Brewery and recommend the Rogue Ales Public House and Nicholas' (Middle Eastern food). Rogue is in the Pearl District, Nicholas' is on Grand (east of the river) and is relatively close to Rain City Bike Shop and a block from Bike-n-Hike. (I can't say much for the bike shops---haven't spent much time in either.)