What we refer to as the ROOT is not the top directory. In windows, this is where you end up if you go to the drive by clicking on the drive-icon...
You need to read and follow the install guidelines found on
http://www.rockbox.org, the manual would be a great place to start.
Rockbox consists of:
1) a bootloader: you 'patch' an original firmwarefile, put it on your device and use the original firmware to 'upgrade'
2) the actual rockbox software: this is a bunch of files that you copy on the drive. Just unzip to the player and you should end up with a directory called
.rockbox on it. If this does not exist, the bootloader will always start the normal firmware.
have fun!
Peter