Using Cubik Studio to model Living Entities for Minecraft

[ZDoctor]

I have successfully modeled and rendered an entity into a Minecraft world, the java file needed heavy editing, but no problem. The problem is that my rotation points are off and I'm having trouble getting them to be correctly placed in the world while also rendering correctly. It feels like there are some unseen equations that are offsetting my models or something. Is this documented somewhere? Is there some resource that I can look at to understand the math used to determine the position of rendering?