Unfortunatly, there are more files than just in the NanoFXv2 directory.
I'm suprised that BCMI isn't working correctly, at all. While I don't completly like it, it "works" most of the time, I've never seen it fail in this manner.
Right, create a directory you can easily find again, and pont BCMI to that.
Then, install it (to the newly created directory) and copy all directories created by BCMI to the root/base directory of BC. You may want to back up the scripts/MainMenu files.