On the right side of your desktop's tasbar (where also the Windows clock resides) you can find the icon for the Multi-Timer Ultimate. It is a blue stopwatch image.
Left-click the tray icon to let the program window appear or disappear.
Right-click the tray icon, to produce the context menu, where you can call the settings dialog, show / hide the program window and exit the program entirely.
Clicking the program window's "Close" ("X") button will not shut down, but only hide the program window.