As terdon says, there should be a hidden config directory for mathematica in /home/fred or /home/fred/.config. To have the same configuration for root as for fred you have to make a symbolic link to the config-directory:
sudo su
cd
rm -r ./mathematica-config-directory
ln -s /home/fred/mathematica-config-directory
exit
Note that everytime you are using mathematica as root and it creates a new file in the config-directory you won't be able to change this particular file as user fred. In this case you have to change the ownership of the mathematica-config-directory back to fred with the following command:
sudo chown -R fred:fred mathematica-config-directory