I study my reference photos or the live model and determine where the strongest lights are.  I have established some of the shadows when transferring the sketch and they remain visible.  I will reinforce them as I proceed but this stage is all about the surfaces which catch the light, thereby identifying form and dimension. I do not attempt to paint any strong highlights but only map out the three dimensional quality of the portrait.  Some artists work with strong tones but I prefer to continue with pale shades until I am sure the likeness is very accurate.  My belief is that using the under painting and tonal surface of the canvas to become the shadows, at least until the painting is developed somewhat, makes a more satisfactory skin tone.  Some of my earlier works were not done that way and I can see the difference.