doesnt make any difference if you are in a subfolder unless you had the baseurl wrong you can change the branding in download.php...
PHP Code:
$name = $row['filename'];
$friendlyurl = str_replace("http://","",$site_config[SITEURL]);
$friendlyname = str_replace(".torrent","",$name);
$friendlyext = ".torrent";
$name = $friendlyname ."[". $friendlyurl ."]". $friendlyext;