Rigging WP as an Encyclopedia

I’m looking to setup WP to function as an encyclopedia. The example I have in mind is the featured site: the Internet Encyclopedia of Philosophy (link).

The way this site manages content (especially the table of contents feature on every page) is exactly what I’m looking to set up example here). I can setup the template to function/look like the IEP website. However, I do not know how to organize the actual pages to fall within a linked Table of Contents and arranged headers as is the case with the IEP. If anyone could give me a few pointers, it would be greatly appreciated.