1. Mix together the yeast and warm water and let it sit for 10 minutes.
2. Place the 3 cups of flour, salt and sugar in a mixing bowl (or food processor, if you are using), and knead until you have smooth dough.
3. Cover the dough with cling wrap and leave it in a warm place for 3-4 hours to proof. The longer it proofs the better.
4. Shape the dough in a ball and roll it with a rolling pin over the whole wheat flour.
5. Grease lightly the pizza pan and place the rolled pizza over it, apply the toppings and bake in a preheated oven at 350 F until ready.
If the bottom is taking longer to cook, remove the pizza pan from under the cheese pizza and finish cooking the pizza straight on the racks.