Start Transmission in the background
Run as
transmission --minimized
This will launch it minimised to the notification area. For more information check out the man page
man transmission
For latest Ubuntu use
transmission-gtk --minimized
install this Package: transmission-daemon (and the associated control interface transmission-remote)
$ sudo apt-get install transmission-daemon
So you can start it as a daemon (in the background) and use transmission via browser (transmission-remote)
Ciao.