We booked out of Seattle because the airfare was so much more affordable than Vancouver. Checking in was easy in port. I suggest arriving the day before - there were people that almost missed the sailing because of delayed flights in the same day.
The most frustrating thing on board the Rhapsody was the crazy setup in the Windjammer. It was designed poorly and everyone was converging on the same places all at once. We avoided eating there for as much of the trip as possible. We ended up eating in the restaurant for breakfast, lunch and dinnner to avoid the chaos in the Windjammer and that is not normal for us. We usually eat most of our meals there.
Aside from that, the cruise was awesome. We had great experiences with most of the staff. The only siourpuss was one of the cruise director's employees that was a bit crabby. Service was fast at all the bars and at the restaurant. The food was fine, but because it's a smaller ship, there weren't as many choices.
We did our own excursion with Harv and Marv Whale watching in Juneau, and it was great. We also rented a jeep in Skagway on our own. The only excursion we did through the ship was the Hop on Hop Off Bus in VIctoria. It wasn't worth $39, so find your way into town on your own. All 3 cities were great to visit. Don't miss Mendenhall Glacier in Juneau. Wildlife is amazing. Saw a big black bear outside of Skagway, which was a highlight.
The captain was amazing and really maneuvered the ship during our visit to Dawes Glacier in Tracy Arm Fijord.