The application doesn't have any kind of interface. It just appears in your tray bar, and you can manage it from there. Just press 'ctrl T' when you're on the window that you want to remain on top.
Window On Top is a small, lightweight tool that doesn't take up any space, yet brings an interesting feature to Windows. There are many occasions in which it would be very useful to keep a text document, image, or certain application visible. The application is especially helpful on large monitors.