Thanks for all of your help!

I booked the sleeper cars today over the phone and paid cash. I'll book the regional Cascades trains when I need to or when I get the points.

The Amtrak agent on the phone said that they don't know in which order the cars will be in on the train, but I have the car numbers. She said that in most cases they try to orient the cars on the Coast Starlight such that the full bedrooms get the better view. Based on this I selected roomette #6 on the upper floor for both legs (even number roomettes are on the same side as the full rooms). This allows me space from the toilet and not being too close to the doors or stairways at night.