You do NOT normally have to get off (especially if the flight is running late), but you do need to stay out of the isles while the clean the plane. Occasionally they will deplane everyone if the flight is early (its late much more than early).

As far as upgrades, it is a little bit broken in the last few weeks. You might process an upgrade all the way through, but it you dont process the first leg only the SEA ground crew can add you to the upgrade list for the 2nd leg as you wont be on the list (this is a new development over the last few weeks, and seems to affect all the Plats I fly the route with each week). Obviously by the time you get to SEA those upgrades have already processed (They start boarding within 5-10 minutes of deplaning).

The gate agents and President's Club agent in SEA say that they have reported this upgrade bug, so hopefully it will get resolved soon.