I'm not sure Gnome reads this file, but open up ~/.config/user-dirs.dirs in a text editor and make manual modifications. Then log out and back in to see changes apply (or perhaps restart the desktop manager. gdesktop?)
Should look something like this; fairly intuitive.
Code:
# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
#
XDG_DESKTOP_DIR="/home/zorael"
XDG_DOCUMENTS_DIR="/media/main/documents"
XDG_DOWNLOAD_DIR="/media/main/downloads"
XDG_MUSIC_DIR="/media/misc/audio"
XDG_PICTURES_DIR="/media/main/pictures"
XDG_PUBLICSHARE_DIR="/media/main/share"
XDG_TEMPLATES_DIR="/media/main/documents/templates"
XDG_VIDEOS_DIR="/media/main/anime"
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