If you want to do additional customization or add more Vim plugins, create a ~/.janus directory and add your plugins there, either with a git clone or by adding submodules to your own git repository there. This directory is treated like a normal pathogen directory. For example:
$ cd ~/.janus
$ git clone https://github.com/vim-scripts/Rename2.git rename2
Or, if you have a git repository in ~/.janus, you can use a submodule:
$ cd ~/.janus
$ git submodule add https://github.com/vim-scripts/Rename2.git rename2