Use
git clone --recursive git@github.com:nathanmusoke/dotfiles.git
to clone the repository and submodules.
There is a script install.sh included which will create symlinks from ~ to the dotfiles.
This should backup existing files ~/foo/bar to ~/foo/bar~YYYY-MM-DD-HH-MM-SS.
At this point it also needs to be run from the root of the git repository.
I use Pathogen to manage Vim plugins.
To initialize them (if --recursive not used when cloning), use
git submodule update --init --recursive
To add a new plugin,
cd dotfiles/.vim
git submodule add https://github.com/foo/bar.git bundle/bar
To update one plugin,
git submodule update --remote path/to/plugin/
To update all plugins,
git submodule update --remote
Adding a tilde to the end of the directory containing a bundle will cause it to be ignored by Pathogen.