you don't need to put the plutonium app into the same folder as the game files... in fact, i would recommend against it. I've seen more than 1 person break their install by moving game files or mixing plutonium files into their game folder.
Just install bo2 from steam... then put plutonium somewhere (Desktop, C:\Cool, whatever) and then just tell plutonium where your game folder is using the SETUP button... it doesn't need to be mixed in.