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I run transmission in daemon(headless) mode and and then use Transmission remote GUI.
I am sorry i cant help you much with deluge as i havnt used it much my self
Here is a guide that is a little bit outdated but gives you the general idea. Basically any guide to a headless transmission setup on Debian should do the trick.
Just change the download directories to your external drive and make sure the webserver is enabled. Then you can either send magnet links through the webserver, or use a program like this on your PC to send torrents to transmission. FYI, you should probably also set up your PI on a static IP address, otherwise you will have to keep changing the settings on your torrent client.
Use transmission-qt together with TransGUI to have the look and feel of uTorrent together with Sonarr. Transmission is supported by Sonarr.
Install TransGUI on your computer and connect it to the web interface of Transmission on the NAS. You'll have an app on your computer that accepts Magnet links but they'll download on the FreeNAS box.
No, I don't think I explained well. You are using the pi as a server, right? And you connect to it with a normal computer. That's where you use a client to connect to the transmission-daemon that is running on the pi.
You use OSX, right? Try this one http://sourceforge.net/projects/transgui/ (SF is flaky today, it might not load, try later if that's the case)