The Seattle sleepers (730 and 731) and the transdorm are on the front. The Portland sleeper (2730) is on the rear. They'll open up the sleeper that ticketed passengers are in, and both if there are boarding and detraining passengers in both.
I ride the Empire Builder regularly and I seem to recall the Portage is frequently a double spot, at least in high traffic periods with a max consist, although I've never boarded it there (I usually ride it straight through between Chicago and Everett). So the Seattle sleepers will be in the first spot.
Portage is an unmanned stop, so they'll board you, then the tickets will be lifted/scanned after the train is back underway. Chances are the SCA will be the one who boards you, not the conductor.