Two of us went on a 7 day, 6 night kayaking and camping trip in the Everglades. Here's a website with a map of the Everglades Wilderness Waterway 'trail': http://www.nationalgeographic.com/adventure/0201/everglades.html. You can find a lot about the marked trail on the web. You can see our exact route (marked on the satellite images) as well as some photos/videos/stories at http://www.travelpod.com/members/ericavanetten. It was a lot of fun -- birds, dolphins, stars & sunsets (and bugs).
We put in at the Gulf Coast Visitor's Center in Everglades City and paddled to the Flamingo Visitor's Center in Flamingo, about 100 miles away by paddle. No charge to leave the car for the week, or to launch the boats (at Chokoloskee - 2 miles away - there is a charge).
We rented a car in Marco Island, Florida to use to shuttle our car down to Flamingo. Enterprise offers free 'pick up and delivery', so we took them up on it, and arranged to have them drop me off at the launch site after returning the car (Marco Island is about 40 miles away). Nice folks there at Enterprise -- make sure you're friendly to whoever answers the phone and arrange this ahead of time.
To do the trip you need to get permits from the visitor's centers and reserve campsites for your whole trip. http://www.everglades.national-park.com/camping.htm The backcountry permit costs $10, and it is then $2/night per person for each site. A lot of the sites only allow one or two parties, and you can only reserve them up the day of or the day before your trip. In our case it was no problem - there were not a lot of people out there (we saw 6 other people camping the entire trip).
There are plenty of chickees (raised platforms with metal roofs) and sites off the 'trail' itself, and its easy to make up your own route -- either a circular route back to the same place you started or a through trip (for which you should allow about a week). In general it was fine to go off route, but *definitely have a GPS* and get good maps. (Incidently, I have the 3 nautical charts ($20 each) in slightly used (loved!) condition, if anyone wants them to purchase or borrow). There are not many people out there, and if you get off track (and don't have a GPS) you could easily get lost (we did at times!). Its all mangroves (and they all look the same), and no place to camp besides the designated sites -- the ground is not accessible except on the beach sites -- in the park its all stilt roots & deep mud.
About half the time you're going to be against the tides/wind/sun. Just count on it. Its hard to predict the tide influence when you're not on the coast -- we were told the inland tide schedule could vary up to 6 hours from what is experienced at the coast. Paddling against the tides & wind can be tough, but when its in your favor its awfully sweet...
Bugs were unpredictable - completely absent at some sites and horrendous at others (so many no-see-ums you could hear them). They say chickees allow for wind and the absence of bugs - and this may be true - but our worst bug experience was at Joe River Chickee on a still night. Winter is considered the best time of year to go, so go soon if you're interested!
Erica