Why don’t you spend some time familiarizing yourself with the options contained in the preferences? Look there before you ask a question about how to do something, just in case it’s right there in front of you.
(Moved discussion to the BitComet client help forum)
The boss key merely hides the icon. Most windows programs like BitComet require the GUI, so the best you can do is minimize it and hide the icon. Currently there’s no way to do that automatically, sorry.