Why not just set your browser to "Always ask" you where to download the .torrent file, then place the file where you want the downloaded file to finally reside? That way your .torrent file is always with the content and is easy to locate when you move, trash or archive the file.
Guess you have to switch to Firefox - I can't find the option in Safari - but you just might find Firefox preferable to Safari anyway. (I use both, but if I had to pick only one I'd probably pick Firefox.)