I've been there and really enjoyed it, however it's not something you can spend a lot of time there - at least when I was there about 6-7 years ago but still pretty fascinating esp looking inside the Hunley itself.
If you are a Civil War buff, I'd also recommend Fort Moultrie and the Charleston Museum.
"The Battery" is nice and features a number of old cannons on display and is one of the more famous scenic places of the city. There is an Aquarium there as well, but when I went they had not been opened very long or very big. However as I understand it now, it's a lot better. There are a number of ghost tours offered.
Lived there for 4 years while going to college, and how I miss it.
I've been on the Midway, Hornet and Intrepid. I may as well add Yorktown to the list. I have to give the Hunley and Sumter priority. I hope it works out.
Now I'll have to decide whether or not to bring my camera.
Patriots Point is a must. Spent a few nights on board the Yorktown years ago in boy scouts. Great experience I'll always remember, also went out to Fort Sumter too. Definitely hit those two places. Patriots Point alone could take all day at least if not two.