Yeehaaa!
Masking. I LOVE masking. It can be tricky.
For the mouth what you want to do is put the "mouth line" onto a new layer above everything. Set the mouth line layers masking property to "do not mask this layer". The lines of the lips will be on a layer over everything else. The problem is that strokes are included in the mask. You can't stroke a mask shape/layer and have those lines remain visible.
You could also simplify the set up and have the lips or mouth line stroke so it is "inside" the mouth mask. Make the stroke thicker so it shows up inside the mask. This has problems as well. I usually put the stroke on a layer that isn't masked.
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... and sometimes... you don't even need masking at all... for instance:
See that sketch you drew of the neck area?
Look at it carefully. You have the neck area that needs to cover the back of the collar but also be behind the front of the tunic or jacket.
The simplest way to do this in my humble opinion would be to have all those "shapes" on one layer... the jacket/collar shape would be "connected" but the shapes in different orders.
The back collar "shape" would be lowest, then the neck then the front of the jacket.
The back part of the tunic and the front part can actually be connected together... part of the same mesh. The beauty part is that the filled shapes themselves can be in different orders.
(.moho file... same as an .anme file.)
http://www.lowrestv.com/moho_stuff/shape_layers.zip
-vern