Create destination folder in your repository
mkdir -p ~/Documents/<your_project_location_path>/dotfiles/<application>/.config/<application>
Move your existing config files to your new location
mv ~/.config/<application>/* ~/Documents/<your_project_location_path>/dotfiles/<application>/.config/<application>
Remove empty location
rmdir ~/.config/<application>
'Stow' your dotfiles (i.e. create symlinks)
stow <application> # If .stowrc configuration file has been made
stow -vt ~ <application> # under ~/Documents/Projects/dotfiles