Make lots of indexes, or "Maps Of Content".
An index can point to a other pages, including other MOCs. It can also have its own text.
There, that's 95% of it. I have a top-level "Index MOC" page that links to my "Work MOC" (which links to projects I'm working on), "Orders MOC" (that links to a bunch of pages for local restaurants and what my wife likes ordering from them), "Diablo MOC" (because I play a lot of Diablo 3 and keep notes on how to optimize characters), etc.
In short, it's a way to turn a mess of pages into a web of links that I can easily click through if I want to.