It's not particularly configurable, I don't think I can access the full transmission settings from the web interface that comes with it. With Remote++ I can add a list of custom folders to download to, so click magnet, select location from a list that pops up, save, done! Nice.
Definitely enabled in the siphon options, but control click works for me. Just need to sort out the raspy wifi crapping out so often and refusing to reconnect unless you reboot or replug the dongle.
Think I may have it stabilised, it stayed up all night. But I think deluged died, so need a cron to check if it's still running and restart it if not. No idea how to do any of that, though :-D
After I botched the upgrade to rc3 of xbian I did a fresh install of it and decided to try transmission. Mainly because it has an xbian /Xbmc plug in to see how the downloads are doing.
So far with rc3 the network has been much more stable, it's stayed up for 12 hours now without me having to reset the wifi and transmission has downloaded 4 hd TV episodes, previously with rc2 and deluged I'd be lucky to get one episode over night. Also the xbian plug in can pause it while watching videos, I'm not sure how well the Pi would cope playing hd from the USB hard drive while downloading at 300k/s.