Stick things you want to be symlinked into your home directory in "home". A
basic .vimrc, which has pathogen.vim already set up, is there for an example.

Clone it to your system:

$ git clone your-server:dotfiles.git ~/.dotfiles

Run apply.sh:

$ . ~/.dotfiles/apply.sh

You can use submodules to keep track of updates from upstream configurations and
other various modules. For instance, to set up sensible.vim, you could run this
(from your base dotfiles repo):

$ git submodule add https://github.com/tpope/vim-sensible.git vim/bundle/vim-sensible

apply.sh will update your repo and its submodules each time.