Alaska Marine Highway

The AMHS will be expensive if one is taking a big rig or truck/trailer, but IMNSHO, the experience on the AMHS is not to be missed.

SE Alaska is a "whole nother experience" and the AMHS allows lots of flexibility to stay in certain spots for longer periods of time if you want. My bucket list includes taking all the routes the ferry has to offer. I've got SE done for the most part, working on the SC areas (Whittier, Valdez, Cordova, etc) and saving the Western (Kodiak, etc) routes until last.

My suggestion would be to determine when you want start your AMHS trip, where you want to stop for how long (in my view, KTN, JNU, and Sitka are worth multiple days) and when you have to conclude your trip (i.e. in Whittier or wherever you're returning to). If you get that info and pass it on to the AMHS, they'll likely be glad to propose an itinerary around the ferry schedules.

We took the ferry from Prince Rupert to Haines last year. We towed our 24" TT with our GMC truck A total of 49 feet. I made our reservations in March for a June 4th sailing. We stopped for three days in Ketchikan where we camped at Signal Creek CG in the National forest. We had reservations but did not need them as it was almost empty. We reboarded the ferry and continued to Juneau where we camped at Lake Mendenhall, again in the NF. We left our rig there and flew to Glacier Bay to spend the night at the National Park Lodge and do the boat tour. For the 23 hour trip from Ketchikan to Juneau we had a cabin on the ferry. We took our rig off at Haines as we wanted to drive the Haines Highway but we stayed there for five days at Oceanview Campground. During that time we took the passenger ferry to Skagway for a day trip. It was absolutely fabulous and I highly recommend it. I will be glad to send you more information if needed. lizzie

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.

We left Indiana May 20th in 2013 and returned 79 days later. No reservations at all except The Alaska Marine Highway, which were made in early February 2013 for a July boarding. We took 12 days to make it from Skagway AK to Prince Rupert BC, with at least 2 night stops in Haines, Juneau, Sitka and Ketchikan We made the trip in our 21 foot B+ without a toad.