To add a new bundle do (e.g.):
git submodule add http://github.com/tpope/vim-fugitive.git bundle/fugitive
git add .
git commit -m "Install Fugitive.vim bundle as a submodule."

and to update all submodules do:
git submodule foreach git pull

to clone to another machine do something like:
cd ~
git clone https://[email protected]/sdixon99/dotvim.git
ln -s ~/.vim/vimrc ~/.vimrc
ln -s ~/.vim/gvimrc ~/.gvimrc
cd ~/.vim
git submodule init
git submodule update