Holy crap. How long has this been here and I didn't know about it?
Clipping Groups, known in Photoshop as Clipping Masks and accessible from the layer's right click menu, allows you to just use an existing layer's per-pixel opacity as a mask for layers sitting on top of it. So you can do your flats on one layer, then create a layer above it set to Multiply and do your shading, instead of having to mask the whole folder or constantly mess around with the magic wand. This would be really useful if you're trying to do a no-outlines picture. And unlike folder masks, which used to be my go-to method for this, it doesn't add a ridiculous amount of data to your file size, and allows you to go all the way to the edges with SAI's fancier brushes (which you're not allowed to use on masks for some stupid reason).
I'll be putting together a proper tutorial on all the ways this can be useful, but I hope this post was enough to give you a basic idea how it works.