Hi Jack 2007,
I don't have all the answers to your questions, but having gone on an Alaskan cruise from Vancouver I can tell you this:
You actually enter the U.S. in the terminal as you're boarding the ship. U.S. customs will go over your passport/entry documents at that time. You will not have to show documents at the Alaskan ports.
Then, upon return, you actually enter Canada at the terminal as well and the Canadian customs officials look at your documents there and then.
I am Canadian, so all I needed was a passport, but there are different lines for Americans, Canadians and "others" I think.
I hope this helps.