(Click on the thumbnails to get the full size)
First of all, I like to start from the head and work my way to the bottom as a way to organize my thoughts.
1)I opened my photoshop (Sorry Gimp users) and open up this image, you would notice that the layer is locked so just double click on it and press ok. Now invert the image and set it to multiply.

(You are going to have to figure out on your own what kinda of colors you want to shadow with, everyone has their own styles and preferences.I linked some in the Tutorials section if you are lost.)
2)Don't worry about the tones at this point, we will get to that later. What you do have to think about is how to organize the layers you are working with. I find color coding and using folders per facial feature helps the most.
For example: Red:Done, don't touch it unless you really need to!(Usually a seam) Green: Interchangeable with another green in the same category.(I use them for boob options and stomach options. Blue: Add-Ons, or things I am experimenting with.


This is a screenshot of how I organize my Lisa Template, I don't name each and one of the layers, but I do try to group similar stuff together i.e Nose, Lips, Jawline, Eyelids, Highlights, Skull Shadows....so on and so on.
My face template always 512x512, (It doesn't distort) and I submit it that way; I know people use 256x256, but I like to add more details to my skins.