This is the simplest way of doing it and in my opinion the best. You can just have all of the files where they are supposed to be without the need of symlinks or anything. I've been doing it this way (well a bit different but very similar) and it works like a charm.
I explain here the steps of how I do it: https://github.com/josepmdc/dotfiles#2-if-you-want-to-manage...