Use the project install file.
The installer will backup old settings with a date stamp and create symliks as necessary
cd vim
./install
or
cd .vim
./install
cd ~/.vim/
git submodule init
git submodule update
Note: for pyflakes or jedi to work correctly, use:
git submodule update --init --recursive
cd ~/.vim/
mkdir bundle
git submodule add https://github.com/fergusb/vim-foo.git bundle/foo
git submodule foreach git pull origin master
git submodule update
" vim:ft=mkd