Hunley built three submarines. I saw the first one he built (CSS Pioneer) on display in the French Quarter in New Orleans. It was a two man experimantal sub, and his first build.
http://military.wikia.com/wiki/Pioneer_%28submarine%29
Even with the loss of three crews, the Confederacy came out ahead, the Union lost a lot more sailors on the ship they sank.
The Union also had a submarine, intended to transport a diver, who layed charges.