I would vote for an upper seat, too. Lower seats are preferred by some because the compartment is smaller and therefore the crowd is quieter (though I've never had a loud or unruly crowd on the upper deck). Track noise will be louder downstairs, though, and the view isn't nearly as good.
On some trains, a car attendant standing at the door will give you a seat assignment as you board. It's not heavily enforced, though, and if there are a lot of other open seats and/or there are very few other people getting on in your car, you can probably sit anywhere you like (though someone else getting on may come up and say you're in their seat). Once the door shuts, you can move anywhere within that car you'd like. Just be sure that if the conductor has already passed by to check your ticket and give you a seat check, make sure to take the seat check (they stick it in a plastic thingy above your seat) with you when you move.
This isn't really applicable on your short Cascades trip, but for other long-distance travel, if you want to move to another car, it shouldn't be a huge problem, but if your stop is one in the middle of the night and you want the attendant to wake you up, be prepared that if you move to another car, you may not get woken up, since the attendant won't likely be paying attention or may even be sleeping (cars are assigned by destination--you might want to check with the attendant of the other car to see if they can do it). (Sorry, that was a lot of commas for one sentence...)
On another note, I'd be hesitant to reserve a lower-level seat on the Seattle-Vancouver run, since while some trains currently use two-level Superliner trainsets, as the single-level Talgo sets come back into service (they were out for repair), they will replace the Superliner sets and everyone will have lower-level seats (no sense paying for one, then).