Our school also does desertification, and using orange and yellow is probably a good idea because the colours are associated with desert environments and such. Our teacher showed us a past SAC where a student used greyled and a red pencil and it just didn't really look right. If you think your colouring is dark enough so that the orange and yellow is differentiable, then I would think this is the best way to go.
As for the little bits of desertification around the place (if you're using the textbook map, that would be the ones in places such as Italy, Turkey and Madagascar), they are probably less important than the bits that occur right next to deserts, but if you can fit them in to the 6 minutes of mapping (if its worth 3 marks) then it's a good idea to include them, especially if you refer to them in a distribution explanation in the next question or so.