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
https://github.com/QuickBox/quickbox_setup/commit/54f11e85735f0a67996d1d8b63f3e19f3f57cbf9
https://github.com/QuickBox/quickbox_setup/commit/1d356c177b00b392911ff16fd1669312272a5ad2