Think of each layer like a virtual piece of paper, each stacked on top of another. Any part of the layer that doesn't have paint will be blank, showing the layer beneath it.
For example, that Rayne family photo.
First, a pencil sketch:
https://dl.dropboxusercontent.com/u/264375853/Images/Layers/RayneFamily_1.jpgA new layer was created above the sketch, where the cleaner inks go:
https://dl.dropboxusercontent.com/u/264375853/Images/Layers/RayneFamily_2.jpgBecause the inks are on a separate layer, they don't interfere with each other and I won't have to manually erase the sketch later. Just need to make the sketch layer invisible, or delete it. I prefer to just make it invisible though, just for future reference(Like right now).
So, sketch layer is turned invisible, a new layer is created *underneath* the outlines, where all the colors go:
https://dl.dropboxusercontent.com/u/264375853/Images/Layers/RayneFamily_3.jpgBeing underneath, one doesn't have to worry about screwing up the lineart. Just for reference, this is what the color layer looks like without the inks over it:
https://dl.dropboxusercontent.com/u/264375853/Images/Layers/RayneFamily_3B.jpgCreepy stuff.
Anyway, then on some more layers, finishing touches can be added without fear of accidentally messing up the other one, such as eyes, hair, shadows, etc:
https://dl.dropboxusercontent.com/u/264375853/Images/Layers/RayneFamily_4.jpgEach family member gets their own layers, the background got its own layer behind everything else, the frame got its own layer above everything else, even the signature got its own layer, etc. Lots and lots of layers.
So that's how layers work anyway, in the case of the emotes it's mostly for organization, but it does make things easier as well - I didn't have to redraw anything to make that pale skin base(Angel/Zin) from the yellow base, just had to copy the yellow base layer(Which has no face on it) and drag a slider bar to change the color. Each face has its own layer so none interfere with the base below it.
Here's a video that might explain it a little better:
https://www.youtube.com/watch?v=eIcYWEQH4z4It's for PS, but the principle applies to pretty much any program which supports layers, such as Manga Studio, Gimp, etc.
