In a nonstick 12 in skillet; cook sausage over med high heat until no longer pink; drain.
In same skillet; cook pepper and onion for 5 minutes or until tender.
3In a 4 quart saucepan, melt butter over med low heat. Stir in flour, salt, and 1/2 teaspoon of the pepper flakes.
4Cook and stir until smooth. Gradually add milk and water, stirring constantly until thickened. Gradually add Cheddar cheese; stir until melted.
5Add macaroni, sausage and onion mixture; stir to coat. ( I pour it into a big bowl to mix it).
6Pour into casserole. Sprinkle with Mozzarella cheese.
7Bake uncovered 35 to 40 minutes, or until bubbly.
8Top with Parmesan cheese, pepperoni and remaining 1 teaspoon of pepper flakes. Bake until lightly browned, about 5 minutes. ( You can add whatever you want to this dish..mushrooms, italian seasoning...I added garlic powder, onion powder and oregano to the meat..and a little parsley flakes).