Preheat the oven to 450 degrees F.
If using ground beef, saute onions and ground beef on the stove. On a baking sheet, toss the peppers, zucchini, squash, mushrooms, and onions (for vegetarian dish) with olive oil, 1/2 teaspoon salt, 1/2 teaspoon pepper, and dried herbs. Roast until tender, about 15 minutes.
Meanwhile, bring a large pot of salted water to a boil over high heat. Add the pasta and cook for about 6 minutes. Since you will be cooking the pasta a second time in the oven, you want to make sure the inside is still hard. Drain in a colander.
In a large bowl, toss the drained pasta with the roasted vegetables, beef & onions, marinara sauce, fontina cheese, mozzarella cheese, and peas. Using a wooden spoon, gently mix, until all the pasta is coated with the sauce and the ingredients are combined.
Pour the mixture into a 9 by 13-inch pan. Top with Parmesan cheese. Bake until top is golden and cheese melts, about 25 minutes.