I just had 3 layers of faces on at once, the reference one was at 50%opacity it was just her standard face, I used it to figure out the exact positioning. It's kinda hard to explain. Anyways, since Alphys has so many good facial expressions, I couldn't settle for just 8, so I used 16 instead (and there are still more I could have used there's a lot of expressions)

Anyways, maybe this image will illustrate what the reference layer is a bit better than I can describe.