Battery Wagner was located on the northern end of Morris Island, southeast of Charleston. Unfortunately, all remains of the site were eroded away by the sea years ago.

You may have been mislead to believe that Battery Wagner was north of Charleston because GLORY incorrectly shows Shaw's troops attacking from the left (i.e., north). I understand that there was a big condo in the way where the movie was shot (not in Charleston) which caused them to have to charge the wrong way.