St John's Yacht Harbor has a courtesy car which can satisfy much in the way of transportation needs. It's quite well protected and is a safe place to keep a boat. We'll be there when this blasted weather clears.
Charleston City Marina is quite a shlep from downtown - we stayed there for month once - never again. They have a van that will take you to a couple of places. The current there is dangerous at mid tide situations.
Charleston Maritime Center is the best situated to walk around Charleston. It's a very small marina though and you can get beat up there in some weather conditions. I wouldn't leave a boat there. We've stayed there for a month too.
Charleston Harbor Marina has the water taxi and a scheduled trolly. We've stayed there for a week at a time and usually are there for a few days each season. We'll be there when this blasted weather clears.
To really help provide suggestions for Charleston, more information is needed about what services are desirable.