The area that the South had an advantage over the North in the Civil War was their military leadership. Their military leaders had a lot of experience and knew what they were doing. They knew the land and everything about it and were very determined, which rubbed off on other soldiers.
The North had a lot of more money than the South and they had access to more ports, so the North was often times more equipped than the South was. Even so, the excellent military leadership that the South had was a scary advantage that the North could not beat.
A lot of the battles that happened during the Civil War happened in the South, so the South was able to have a defensive war. The Confederate leaders knew the land better than the North, so this was an advantage.