You only need one copy of it running.
Then launch SE4
The tray tool will:
1) Remove the black border around the game.
2) Let you click and drag any of the game windows around as if it were a real window.
3) Let you shift-click and CTRL-click in the design screen and the simulator setup, to add or remove 10 (or 50) items at once.
See:
http://imagemodserver.mine.nu/other/...indowedSE4.png