uTorrent (or any other client) needs to check for the exact file or files (or copies) that the torrent was made from.
So for one file in a torrent you point uTorrent to that file.
If the torrent was made from a folder than you would need to have a folder for uTorrent to check.
In short, it doesn't matter where the files are as long as uTorrent can check them.
PS I hope that makes sense…