We went north on the ferry system last year. Like Teacher's Pet we took about 12 days from Prince Rupert B.C. to Skagway. We made our reservations about march for an early June trip.
Look at the AMHS schedule and you can figure out how long you will be in one place. We were 2 or 3 days in most places with only one day in Petersburg. Arrived at 11:00 PM and left next day at 9 or 10 PM. If we waited for the next ferry we would have been there for at least 3 days.
We chose to do the inside passage northbound, so once we arrived in Skagway we were without any commitments to be somewhere on a specific day.
We stopped in Ketchican, Wrangell, Juneau, Petersburg, Haines and Skagway.
The ferry schedule dictates your length of stay at any destination.