Datakoll: I've done it on the Alaska Marine Highway, which I assume is the ferry system you're talking about.
Arrive several hours in advance and tell the ticketing agents what you are doing. They will direct you how and when to load your boat onto the car deck. I recommend using a cart to speed things along, especially if there is gear in your boat. You will not be able to access your boat during sailing, so bring everything you need with you up to the passenger deck.
On arrival, wait for all the cars to depart the car deck, then roll your kayak on down the ramp. In most towns, there will be a convenient dock nearby for you to launch from right away. You could also stay at a hotel or hostel the first night—most are located within walking distance from the ferry terminals.
Again, a kayak cart will make all this much easier.