In my case I have each instance looking at a different folder to "auto load" from. I don't normally browse the web on the machine I seed from so I generally right-click to download the .torrent and save it to the appropriate autostart location (via a network share).
In my case right now I have:
instance 1: general use, seed to 1:1, limited to 35K upload I use this for public trackers where my ratio is not particularly important but I still want to be a "good netizen"
instance 2: boxtorrents, seed to 10:1, limited to 35k upload,
instance 3: what.cd, seed indefinitely, limited to 100k upload (it's incredibly hard to get leechers there so I take as much advantage as I can when I get one).
The advantage of this over setting upload speed limits on individual torrents is that you can apply the limit to a group of torrents collectively instead of just individual torrents. So I can dedicate XXkb/sec to this "group" regardless of which ones are active.
For instance:
I have dozens of torrents for both boxtorrents and what.cd, boxtorrents always has leechers so if I run in one instance all of my upload slots are taken up by boxtorrents so when a what.cd leecher comes along I'm already choked and can't seed to them thus losing out on the opportunity to get seeding credit there.
But by running an instance dedicated to what.cd and another for box the box instance can be choked 24/7 but have no influence over my seeding to the what.cd user that comes along once in a blue moon.
The "By default" seems to stick to the last one that you clicked "yes" when it prompts you for "make utorrent the default...". On the ones you don't want to be default untick the "check when loading" box and they won't try to become default after that.
