To setup your scoreboard on the projector, you want to setup an "extended display" when you connect it to the projector. So that you have the operator screen on your main screen, but then the scoreboard on the extended projector screen.
If you have Windows XP: http://www.wikihow.com/Use-Extended-Desktop-View-in-Windows-XP
If you have windows 7/8: http://support.microsoft.com/kb/976064
Once you extend your display, you can then open the scoreboard window and "click + drag" it over to the extended desktop.