Just link in .bash/index in .bashrc. Be sure to maintain the same directory structure.
The way I like to use it is to just have the git repo containing these files in my $HOME directory (ie ~). I do this with the following:
git init
git remote add origin https://github.com/finkelm/dotfiles.git
git fetch
git checkout -t origin/master
I then use .bashrc for my local-specific scripts/aliases.