The Alaska Marine Highway is the only highway that connects all Southeastern Alaska towns. It's fairly easy to design your own customized point to point itinerary, but be mindful of departure and arrival times. First, decide how long you want to stay in each place. Then, check out all the options on the ferry schedule. Book your ferry before your flight.
RESERVATIONS
If you need to reserve a cabin or you are traveling with a car, it is important reserve ahead. Either will add significantly to the fare, with staterooms generally being the less expensive of the two. This can easily be done at the AMH web site, but make sure you reserve everything you need on each segment.
CABINS
For longer trips they also offer cabins which rent by the room and not by the person. Most have private bathrooms. Rooms with three berths or larger are likely to be arranged with beds side by side instead of bunk style. The Kennicott has many very inexpensive roomettes which provide a private booth/bunk bed setup using public bathrooms.
THE SITKA ROUTE
You get a real bonus with a ferry trip to Sitka from Juneau. You will pass through not one but three narrows. Peril Straight is the most famous and narrow. Olga and Nevis Straights follow. You can often feel the Pacific swell between each of the three straights. These are great wildlife viewing opportunities. We saw killer whales and bald eagles on this route. Look closely at the mouths of creeks for brown bear. Bring binoculars!
Ferry service to Sitka is very regular in the summer, but arrival times are all over the clock. At least one sailing a week from Juneau will arrive and depart at a reasonable hour. We found that the best strategy in Sitka was to arrive on an afternoon or evening ferry, spend the night, and depart on the northbound the following evening. This gave us 24 hours in Sitka, and Peril Straight during the day and the night. These trips on the main line ferries are 8-9 hours from Juneau. The northbound ferries will continue on to Haines and Skagway.