For the sauce: In a large heavy skillet, heat the oil over medium heat. Add the pancetta and cook, stirring constantly, until golden brown, about 5 to 7 minutes. Using a slotted spoon, remove the pancetta and reserve. Add the onion and cook for 5 minutes. Stir in the garlic and red pepper flakes and cook until fragrant, about 30 seconds. Add the tomatoes, 1/2 teaspoon salt, 1/2 teaspoon black pepper, and the cooked pancetta. Simmer, uncovered, over medium-low heat until the sauce thickens, about 15 minutes. Stir in the cheese and season with salt and pepper, to taste.
For the meatballs: Position an oven rack in the lower 1/3 of the oven. Preheat the oven to 400 degrees F. Line a baking sheet with parchment paper.
In a large bowl, combine the onion, 1/2 cup parsley, 2/3 cup Parmesan, bread crumbs, egg, ketchup, garlic, red pepper flakes, 1 teaspoon salt, and 1/2 teaspoon pepper. Add the beef and veal. Using your hands, combine all ingredients gently but thoroughly. Shape the meat mixture into 16 (1 1/2-inch-diameter) meatballs and place on the prepared baking sheet. Make a hole in the center of each meatball and place a cube of mozzarella inside. Reform the meatball so that the mozzarella is completely covered with the meat mixture. Bake the meatballs for 15 minutes until cooked through.
Bring a large pot of salted water to a boil over high heat. Add the pasta and cook until tender but still firm to the bite, stirring occasionally, about 8 to 10 minutes. Drain and place in a large serving bowl. Add the meatballs and sauce. Toss gently and season with salt and pepper, to taste. Sprinkle with the remaining parsley and Parmesan.