Normally I keep torrent downloads in a separate folder, and copy them to different folders when the torrent is finished. Changing the files will affect uploading, it'll invalidate the torrent info that describes the underlying files.
Some sites like mininova.org allow downloaders to add comments which helps verify files. Also, check the dates of when the torrent was uploaded, if it's been up for a while and has lots of downloads chances are it's OK. Finally, run anti-spyware/virus scans on the files.