Basically you run it and it sits in your tray, then you can change the transparency by either right clicking any window and clicking a percentage, or using hotkeys (like Control+Shift+0/1/2/3/etc.) In addition to handling transparency, it can also making windows always on top, like AlwaysOnTopMaker. Just right click on a program and press down the "On top" button."
That's about all. There are options, like editing how the right click on a title bar works, edit the keyboard shortcuts, make Glass2k run on startup, beep on glass change, or finally to remember the transparency of every window.
And last but not least, it also can control the transparency of the taskbar! Just go to settings and there is a bar you can drag to your liking, or you can just click on the taskbar then use the shortkeys.