Lile Hanson has created an excellent tutorial on using the new GLSL preview feature. He shows you how to combine different layers, by painting them onto your model in Texture Paint mode using the paint brush. This is similar to masking two photos in Photoshop. I've been wanting this feature for a long time and it's great to see it implemented in Blender.
"Here is a 35 minutes Blender video tutorial about using the new GLSL preview features of the Apricot builds, applied to texturing a head, in a way that could be called multi layered projection painting.
We are going to see the steps to interactively blend together three projections of reference photography into a final texture. This assumes that you already are comfortable with blender, mostly with UV mapping, materials and texture channels. You will need a recent blender apricot version."
Blender Tutorial, texturing a head with GLSL preview from lile hansen on Vimeo.