In a large skillet, caramelize the onions by cooking on medium low heat in 2 tablespoons of olive oil for 15–20 minutes or until golden. Add red and green bell peppers, zucchini, and remaining 1 tablespoon olive oil to the onions. Continue to sauté 8–10 minutes, until the peppers and zucchini are tender.
Meanwhile, cook 8 ounces penne pasta in boiling water for 10 minutes or until tender; drain. Return hot pasta to pan; add vegetables and basil pesto sauce. Gently toss ingredients together to coat. Heat through for 5–10 minutes. Lightly mix in 1 cup shredded Italian cheeses and serve.