The MA (mod author) did release a June 21st patch because there was an error for those who don't own City Living. I don't touch the other folders (unless deleting content I don't want) from within that main folder and everything works fine for me. Then, I take that entire folder and just drop it into my mods folder.
For SoL, I extracted the content to its own folder (using WinRar). I put one folder into my mods folder called MC and placed all of the script and package files in there for MC.