I'm using MGSO but prefer Connary's texture replacer. I have registered the bsa files that are included with Connarys textures. But they don't show up in game. Does anyone know what's the problem?

Unpack the bsa files and overwrite the textures.

BSA don't work very well, it's better if you unpack them with something like http://planetelderscrolls.gamespy.com/View.php?view=utilities.detail&id=28 and then overwrite the old textures.
EDIT: Hicks said it first.

Thanks for the help.