There's only one box, and you add it to vagrant with "vagrant box add develop path/to/develop.box". After that, you can delete the develop.box file from your computer: it now exists somewhere in the nethers of vagrant's configuration.
I guess the main thing I can't get is say I have custom nginx settings or MySQL settings I need in a project. Do I setup those through Chef?
Thanks for the article, lots to look into.
If it's something specific for a project (i.e., a jekyll website), I just write a quick shell script to install jekyll in the Vagrantfile for that project instead of repackaging the whole box.
As for your second question, yes, you would have a specific Vagrantfile/box for a project where you need a specific enviroment. My "develop" box is a general case.
Here's a (slightly modified) example of a Vagrantfile that I use with a project: https://gist.github.com/taylorlapeyre/5399974