Yup we did, although took it from Haines TO Skagway.
Our rig at the time was a 40 ft. MH towing a Honda Element w. a canoe on top. When we decided to leave Haines (after a number of weeks there), we took car up to the ferry terminal and purchased our tickets a day (or two) ahead of time.
The ferry we were to take was to depart Haines for Skagway at around 6 or 7 a.m. and we were instructed to bring our MH and car to the ferry terminal staging area (big parking lot with rows of painted lines for cars and trucks and RV's to line up in) the evening BEFORE the a.m. loading and departure, SOOOOO we moved from our campground in Haines over to the ferry terminal around 8 or 9 p.m. the evening before and dry camped in it overnight.
Since ya HAVE to load RV and tow car separately we'd already disconnected the toad. The only other thing to prepare is that if ya have LP (propane) on your rig, ya MUST shut OFF the tank. When ya do this is up to you, BUT..before they begin loading all the lined up vehicles some terminal worker will come to your rig to physically check and confirm your LP tank is OFF, and will affix a plastic seal to that valve.
Anyway, when time comes to load, I drove the MH home onto the ferry as directed, and my wife drove the toad. There will be a ferry employee walking in front of you when ya load the RV and all ya gotta do is to ABSOLUTELY follow his/her instructions and hand signals. It sounds spooky especially if ya have a bigger rig, but you'll discover its MUCH MUCH simpler and easier than ya think. You're tow car may or may not be right behind ya on the ferry deck, but it doesn't matter when you off load you can simply stop in the unloading area (big lot) and hook up and take off.
By the way, our fee for this trip was $248.00 for 40 ft. MH, Honda car, and two people (wife and I). Don't know what the fee is now, but you may already know.
At any rate, whether going TO Haines from Skagway or the reverse, it's a great route in to or out of Alaska. AND....for what it's worth, we found Haines to be one of the best kept secrets of an Alaska trip.....GREAT scenery, Eagles everywhere, stream and/or lakeside fishing is fabulous, Grizzly viewing great, Moose viewing likely, and take a drive out to Schnabels, Big Nugget gold mine for a day. Ya won't regret the adventure.
Have a great trip!!
Steve & Lynette
2014 Newmar 3103 BAYSTAR/Triton V10 w. Banks/05 Honda Element toad