The hitboxes, attachments and bone controllers are all in the qc. Most of them are all straightforward and can be refined with a little trial and error. This is what he means by code Damaera. The hitboxes are 3d coordinates of a box to a certain bone. The attachments are 3d coordinates of a point to a certain bone.
To make a skeleton you just select joint, and start placing bones in the order of linkage.
To branch off, select the joint and start placing bones again. Study the esf skeleton and follow the same basic patterns.
Start with a base bone and work your way up the spine, and then do your limbs. Make sure you name all your bones. Then you select a bone and select the vertices you want attached to it, and hit assign. Your model will not compile if there are unassigned vertices.