your digi-inks on a layer above the pencils! Helps to reduce the opacity of
the pencil layer.
your basetones on a layer under the inks, with a 100% opacity brush.
shading above basetone layer.
highlight above or below shading, depending on your preference.
the transparent area of the basetone layer, or select the opaque and invert
each layer and delete whatever sticks out, but don't do this on the ink