We've been on the Alaska ferries a number of times. Prince Rupert loads from the back. Ketchikan, Wrangel, Petersburg, Juneau, Skagway, Haines, Valdez and Whittier all load from the side. I think Homer does too but wouldn't bet the farm on that one. Except in rare instances you will not be asked to back your rig on. This is only when they are full or for the very last 1 or 2 rigs loaded and the crew will ask you how your skills are before getting you to do it. They pick the guys who say they have no problems backing. I had a 38' bounder and the crew asked me if I thought I could turn it around inside the ferry to help with a later offload. Piece of cake with their help, but be prepared to swing in your mirrors in if asked, and to deal with clearances of 6" or less when they move you around and things get tight. Again, they are GOOD and we had no problems. SLOW is the word of the day. Go very slow and don't panic. Just watch their directions and and spotters.
Traveling by ferries is a ball. We found the food was good, relatively inexpensive, and the accommodations comfortable. You will have to have your propane turned off and they will seal it with a piece of tattletale tape to be sure you don't turn it on, but our gas/electric fridge stayed cold for hours and the freezer was also fine. Some people have had issues with overhanging rears or hitches dragging when loading at extreme low or high tides, but if ferry personnel can and will adjust the ramps for you, and they have shoring available so there is no problem. Skagway at low tide going from the unloading dock to the main dock might be a problem, but go slow and they will shore the angle up if necessary.