Crust: Proof yeast in water with sugar; in a food processor or in a bowl, mix 2 cups of the all-purpose flour, whole-wheat flour and salt; add oil to bubbly yeast mixture and stir or process into flour mixture until dough pulls away from sides of bowl.
Scrape dough onto floured work surface and knead until smooth and elastic (or process until smooth and elastic), using up to 1/4 cup more all-purpose flour, if needed, to keep dough from sticking.
Place dough in oiled bowl, cover with plastic wrap and allow to rise, in warm place, until doubled; punch dough down, wrap it well and refrigerate until needed.
Sauce: In a skillet, saute onion and garlic in oil until soft; reduce heat to low and add tomatoes and their liquid; break up the tomatoes slightly and add the salt, sugar, pepper, and pepper flakes; simmer, uncovered, stirring occasionally, until very thick, about 30 minutes.
Topping: Cook spinach in covered saucepan until wilted, about 3 minutes; drain, rinse with cold water and squeeze dry; chop coarsely; saute garlic in hot oil for 15 seconds; add spinach and cook, stirring, for 1 minute; set aside.
In a small bowl, mix the cheeses and set aside.
Assembling: Move oven rack to lowest position and preheat to 475°; grease a 9" springform pan and sprinkle with corn meal.
Roll half the dough out to a 12" circle; reserve other half of dough for another use; line the bottom and sides of the pan with the dough, but don't let any dough hang over the edge; spread 1 1/2 cups of the cheese mixture over the bottom of the crust.
Spread tomato sauce evenly over the cheese; spread spinach over the tomato sauce; sprinkle with remaining cheese; arrange the tomato slices vertically, along the side of the pie, alternating the slices with the basil leaves.
Place the remaining tomato slices in a circle in the center, alternating with the pepper slices, interspersing red and green strips; bake for 25 minutes or until crust is golden and filling is bubbly; let set 5 minutes before removing side of pan and cutting.