Currently there is a downloads section in the panel and if you click on it you get a rtorrent item to select and then under that you see the deluge dir.
The directories on disk should probably be laid out like:~/torrents/rtorrent~/torrents/deluge
You're right. Having /deluge/ directory stored within the standard /torrents/ is a recipe for error. This will be addressed in the next version.
I just pushed these changes to testing. Will be in the next release