Hi Mark --
*Usually* you simply add the issue using the next variant letter in the alphabet. Sometimes, however, there are so many variants for a particular issue that ComicBase runs out of letters of the alphabet for the variants. (See the infamous "Crisis of Infinite Godzillas" thread over on the old message boards for more info on that.)
For which specific comic book issue are you trying to add a variant?
EDITED TO ADD: The mechanics of adding the issue and scan etc to your database are covered in ComicBase Livestream #14 starting at roughly the 30 minute mark.