Preheat oven to 400 degrees F (205 degrees C). Place sliced onion and squash in a roasting pan. Sprinkle with rosemary, salt, pepper, and 2 tablespoons of the olive oil; toss to coat.
Bake in the preheated oven for 20 minutes, or until onions are lightly browned and squash is tender; set aside.
Increase oven temperature to 450 degrees F (230 degrees C). On a floured surface, roll each ball of dough into an 8 inch round. Place the rounds on a baking sheet sprinkled with cornmeal (you may need 2 baking sheets depending on their size). Distribute squash mixture over the two rounds and continue baking for 10 minutes, checking occasionally, or until the crust is firm. Sprinkle with cheese and remaining tablespoon olive oil. Cut into quarters, and serve.