i always found the original bittorrent good if you're running via console (say over SSH) or locally you can open a new terminal for each torrent. I believe you can do the same with bittornado, just open another instance for another torrent.
That's why i use azureus though, can manage them all in one
, plus it has a built in tracker and can create torrents, i haven't found anything else that can do that yet.