Transmission

Use -g (or --config-dir) as a switch to transmission-daemon and that will specify the path where config files and such will be placed. This will enable you to have several completely independently running transmission daemons.
Another switch to consider would be -p (or --port) for the RPC port, a.k.a port that GUI-clients talk to the daemon on. The rest you can set via transmission-remote, webui or other various clients.

Personally I would recommend Transmission Remote GUI for accessing the daemon, it tries to be a uTorrent look-alike.

If you want automated RSS downloading then I highly recommend Flexget with the TransmissionRPC plugin to python.

Does it give any errors during the auto-start time, or does it not even try to start it? I don't use Ubuntu so can't really say where to look or for what.

Sky, does it start manually doing this:
the -f option should give console output of what is going on.