Each fade is stored in its own file, called a fade module.  All the fade modules (both installed and disabled ones) are stored in the "MSG Fades" folder in the system folder on the startup volume.  (You can’t change the name or location of the folder, or Shutdown FX will not be able to find the fade modules.)

There is nothing magical about the fades that came in the Shutdown FX package.  You can rename them if you don’t like my naming scheme, and you can delete any that you know you’ll never use.  If you’re a programmer yourself, you can create your own fades and add them to the "MSG Fades" folder.