If you're running nautilus in as root, you'll see root's Desktop folder. Yours is likely in /home/yourname/Desktop (and the rest of your files are probably elsewhere in /home/yourname/)

You can use symlinks to make them available, but operating at root is usually not a good idea. Better to use sudo to run commands as root while logged in as your regular old user self.

In nautilus you can use go > location ... or ctrl-l to view and change the full path to the directory you're in. So do ctrl l and then just type in /home/yourname/Desktop to access the files in your own user desktop directory.