Draw your digi-inks on a layer above the pencils! Helps to reduce the opacity of the pencil layer.

Paint your basetones on a layer under the inks, with a 100% opacity brush.

Primary shading above basetone layer.

Primary highlight above or below shading, depending on your preference.

Select the transparent area of the basetone layer, or select the opaque and invert selection.

Go to each layer and delete whatever sticks out, but don't do this on the ink layer.