MBW--I don't like to pay the owner of the marina $10 to launch, $10 to land, and $10 overnight parking. Therefore, I and many others launch through an opening on the East side of the causeway about 900' before the marina. We park on the West side of the causeway just before the marina, just before a 4' mound with a utility box on it. I've parked there for years w/o problem. This Google image should help.
If you do launch for a day in Chokoloskee Bay, you want to be very careful--very shallow in much of the bay and LOADED with oyster bars in some areas. The large area south of Chok is full of oyster bars. Check it out on Google Earth before you go. It is not an area where you can sail at high speed for any distance.