My husband and I sailed the opposite way that you are going to sail - Whittier to Vancouver, on the Princess Coral. What a SHIP! We had a mini-suite on the Dolphin deck. A balcony is a must for this cruise and you won't be disappointed. We were on the starboard side. I, too, was confused about where our room should have been but, when you near the glaciers, the boat turns around and you also have views on both sides of the ship so that you can see what's going on. We had a WONDERFUL time! I would book starboard on your trip, because that is the side that will be facing the coast.
Make sure to take the Whalequest tour when you're in Juneau; we saw lots of whales and their calves when we went out and it's a really nice tour. We took the small plane ride to have the Dungeness crab lunch in Ketchikan; we didn't see much because it was raining, but the crab was scrumptious! Bring a really warm sweatshirt and a rain slicker, too. When we went to glacier bay the weather was stupendous, Juneau's weather was, too, but Skagway and Ketchikan were rainy and drizzly. It doesn't spoil the fun, though.
We loved the cruise on Princess so much that we're going to Greece next June on the Princess Emerald!