It's time to create a new layer over the background one. It must be in Multiply mode for what we are going to do next.

First choose a light source. This is very important because it will define how your shadows will look like in the finished illustration.

So grab a neutral grey and in that new layer, quickly sketch the shadows you want in your drawing. You don't have to draw precise shading now, this will just be a general idea of how you will apply the tones later.

You can do the same when using traditional tones, by making a copy of the original inked drawing, and using a pencil to define the shadows. I believe this step is very important when using real screentones, this way you can accurately use the tones you need and not waste them.

Now we can start to apply the tones, yay!