Yeah, .skin files contain all the info on where the textures are assigned on a model in JA and JO. While it may look daunting at first, it's relitively simple to edit. You just have to know where everything goes.
Refers to the face of the model (head_face). After the comma: that's the actual path. The models folder, then players, then skin (you can change it's name as long as you change all references to it in the skin files and folders and such. Say you're editing a stormtrooper. You would change the folder's name from "stormtrooper" to "your_skin's_name". Then you would do the same in all the .skin files where it makes references to that folder), then the texture (face.png).