Unfortunately you can't go from Lake Murray to Charleston unless you want to perform a James Bond Live and Let Die boat jump. The difference would be the jump from Lake Murray over the two damn's (earthen and concrete backup) would be about 500' long and almost 200' of elevation change.
When the water is high in the Congaree River, which it is now, you could put in either in Cayce at the Grandy Landing or near the Fair Ground at the Rosewood Rd boat ramp. The only problem is that I don't trust leaving my truck/trailer overnight at either location.
My goal after the Charleston run is to launch my boat at one of those ramps and run all the way down to Lake Marion to the marina where we started the Charleston run and back, doing it in one day. That way I can say I boating from Columbia to Charleston.
It has been a number years since I have done the trip so my intell is poor. As for storing trucks/trailers while going down and back up to Charleston, there are a couple of places on Lake Marion. Santee State Park is just west of I-95,
http://www.southcarolinaparks.com/santee/introduction.aspx but I'm not sure if they allow over night parking. Two other options on Lake Marion are Lakeside Marina & Resort
http://www.lakemarionvacation.com/ & Lake Marion Resort and Marina
http://www.lakemarionresortmarina.com/ . Since boating to and from Charleston is a popular thing to do, I would image one of the 3 would work. I was hoping to do some investigating this winter/spring but it did not happen.