I don't use a computer to separate my layers for stencils. I do it all myself without the assistance of the Photoshop cut-out tool. So before I put any real time into the final stencil I first do some tests. I see if I should go dark to light or light to dark. Meaning sometimes it works best to make your first stencil(the base) black and get lighter with each progressive layer. Or you go light first and end with black.
I used to use the Photoshop cut-out tool, but now there's a million other artists that have discovered it and everyone's stuff looks the same. Also, the updated version of the cut-out tool lost some of the rawness of earlier versions. But as with most Adobe programs it's two steps forward, one step back.