Prepare crust: In a large bowl, dissolve yeast and sugar or honey in warm water, then add the 3 tablespoons olive oil and the salt.
In separate bowl, mix flours together. Add them to liquid mixture, stirring first and then kneading to incorporate. Let dough rise 30-40 minutes. While dough is rising, saute sliced onions in a pan over medium heat with a little olive oil to caramelize their sugars. Cook until transparent but not browned. Reduce heat, add a little water to prevent browning, and let cook another 10 to 15 minutes until glossy and sweet. Add sliced peppers and cook 5-10 more minutes.
Once dough has risen, preheat oven to 425°. Divide dough in half. On clean, floured surface, roll out two round, 12 in. pizza crusts, using fingers to roll the perimeter into an outer crust edge as thick as you like. Using a spatula, slide crusts onto well- floured pans or baking stones. If using fresh tomatoes, layer cheese evenly over crust, then scatter your favorite toppings on top, finishing with the herbs. If using tomato sauce, spread over crust, top with cheese and then other toppings.
Bake pizzas in preheated oven for 15 to 20 minutes, until crust is brown and crisp.