From the manual (the numbers are mine):
"1) When rendering, the first skin can be changed through the entities' skin parameter.
2) This way certain model faces, for instance the clothing, can be drawn with different skins.
3) Faces not assigned to the first skin are always drawn with their assigned skin, regardless of the skin parameter."
As best I can tell, statements 2 and 3 are true, but statement 1 is not. I think it should read "the displayed skin can be changed through the entities' skin parameter."
I have been trying to change the skin only on my model's mouth, so that the mouth can be open when she's supposed to be talking. I can do this if I make the first skin (the first skin listed in Skin Manager) be a skin with the mouth open and I use "Set skin" to assign it to the faces that make up the mouth area. The rest of the skin is just a solid color. The second skin is just a normal skin (the whole body and clothes) with the mouth closed (and I use "Set Skin" to assign it to all the other faces on the model.)
When the skin on this model equals 1, I see the open mouth and the rest of the body/clothes are normal. So the body/clothes are coming from the second skin. When skin = 2 on this model, I see the seocnd skin in its entirety (mouth closed.) If statement 2 was true, and I was actually setting the "first skin" to skin 2, then those faces around the mouth that are not assigned to any portion of that skin would revert to the skin (skin 1) where they ARE assigned. In other words, the mouth would still be open and I would see no change.
The whole thing is a little difficult to explain and I think you don't really get it until you work with it some. I think the explanation should emphasize that there is something special about the model's first skin, mainly that it is the skin where unassigned faces can "peek" through from the skins where they are assigned. This does not seem to be possible with any other skin in the model, no matter what the entity.skin value is.