Shading the pants

Still on the Pants layer check the little 'keep transparency' box in the layer view. (This will make sure that transparent pixels stay transparent and opaque pixels stay opaque.)
Grab the pencil and the dark color and start drawing on shadows. Depending on the size of your doll you might want to start doing the bigger shadow areas with a bigger brush. I use a 3x3 circle on this one and finish off with the 1x1 circle.
And remember, CTRL+Z (undo) is your friend ;)

This is what my pants look like now:

Then I use the darkest color, adjusting the dark and medium color here and there (remember to press down CTRL to get the color picker for fast color change) and she looks like this:

Now I get the light color and draw highlights on the medium colored areas where I see fit:

Then I add the lightest color:

I make the Pants Outline layer visible again and check the keep transparency box. I use the pencil tool with a 3x3 circle brush and the darkest color from my palette to lighten the outline on the parts where it is next to light pixels (on the top of her belly and by the feet). If there's a lot of contrast on the palette I might even lighten the outline one tone more on the lightest places.
Now my doll looks like this in 100% view:




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