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Preheat oven to 400°F. Grease a 3-quart shallow baking dish; set aside. In a Dutch oven, cook pasta according to package directions, adding bell peppers (if using) for the last 2 minutes of cooking; drain. Return to pan.
Meanwhile, for cheese sauce, in a medium saucepan, heat butter over medium heat until melted. Stir in flour, salt, oregano and garlic; cook and stir for 1 minute. Gradually stir in milk. Cook and stir until thickened and bubbly. Cook and stir for 1 minute more. Remove from heat. Gradually add American cheese and Cheddar cheese, stirring until melted.
Add cheese sauce, mozzarella balls, and pepperoni to cooked pasta; stir to combine. Transfer mixture to the prepared baking dish. Sprinkle with Parmesan. Bake, uncovered, about 30 minutes or until bubbly and browned. Let stand for 10 minutes before serving.