It can be confusing at first, but I’m sure you’ll get it once you’ve done it a couple times 
Here’s a small explanation I did for transparent materials:
http://discourse.stonehearth.net/t/more-lights-from-mel-and-other-modelling-stuff/21288/68?u=relyss
The existing materials are inside data/horde/materials, and they reference shaders on the data/horde/shaders folder.