AFAIK TK, the sky mods are different. You need to put them directly into the main SBProPE folder (the hidden one), and rename the one you want to use so that it replaces the original (IIRC the original filename is d5 except for low vis settings and possibly different for the desert themes). It's a while since I did it and can't remember the exact filepath, but it's fairly easy to find. Sorry I can't give you presice details offhand.