To caramelize the onions, heat the olive oil in a heavy skillet, add onions, garlic and herbs. Cook over low heat for 45 minutes or until onions are soft and most of the moisture has evaporated. Discard the bay leaf; add salt and pepper to taste.
To roast the bell peppers, core, cut in half and place on broiler pan skin side up; preheat broiler to high and place peppers under broiler for 10 to 15 minutes or until skin blackens. With a pair of tongs, place the cooked peppers in a paper bag, fold top closed, and cool for 10 minutes. When cool enough to handle remove skin and slice into thin strips.
To roast the eggplant and tomatoes, preheat oven to 400 degrees. Spray an ovenproof pan with non-stick cooking spray; add the eggplant, tomatoes, basil, capers and drizzle with olive oil, place in oven and cook for 30 minutes, stirring once or twice. When eggplant is cooked, add pepper to taste.
For the toppings, finely mince the fresh herbs or crush the dried herbs; add the herbs to 3 tablespoons olive oil and warm until herbs are fragrant. Set aside while preparing crust.
In a small bowl, sprinkle the yeast and sugar over 1 cup warm water; stir to mix. Allow to stand for 5 minutes or until bubbly. In a medium size bowl, combine the flours and measure 1 1/2 cups; set aside. Add the salt to the remaining 1 1/2 cups flour; stir in yeast and oil. Gradually add the reserved flour until dough is soft but not sticky. Knead until smooth; place in a bowl that has been lightly oiled with olive oil. Allow to rise for 20 minutes or until double in size.
While assembling the pizza, preheat oven to 475 degrees; oil a large pizza pan (15 inch) with olive oil. Turn dough onto a lightly floured surface and knead for 8 to 10 times; roll into desired size, stretch dough to sides of pan forming crust around the edges.
Brush dough within 1/4 inch of crust with olive oil and herb mixture, top with crumbled feta cheese, onions, eggplant mixture, bell peppers and olives. Sprinkle parmesan cheese over all and lightly drizzle with 1 tablespoon olive oil. Bake in preheated oven for 15 to 20 minutes or until crust is lightly brown.
Serve immediately with additional parmesan cheese and red pepper flakes.
Pleasse Note: Do not put hot toppings on pizza crust. Toppings should be at least room temperature.