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The main concept is that I think of the facial features as 'stickers' that I place on the main body texture's face. I use multiple UV channels and textures to simplify the process. I think of these textures as 'sticker sheets', and use bone drivers to select the 'sticker' I want.

Are the elements you're moving in this anim part of some 3d UI of the software or are they polygons you created as a way to "remotely" control the bones (or however this is achieved, I don't know this in-depth)?