Sure they didn't include a manual with the program but the options are incredibly straight forward.

There is an option when you first install it to select how to handle right-clicks. If you leave it to 'enabled', it will take full control of the right-click. Set it to "alt+shift" or similar and it will require you to "alt+shift+r-click" to access the glass2k menu. Normal right clicks will work fine.

Also, now that right click works, using alt+shift+r-click lets you set the transparancy level for each program window. Varying amounts from 0% to 100%.

This program is excellent.. people just have to read the options...