Cook pasta according to package directions, omitting salt and fat.
Heat a large nonstick skillet over medium-high heat. Coat pan with cooking spray. Remove casings from sausage. Add sausage to pan; cook 5 minutes or until browned, stirring to crumble. Add onion and bell pepper to pan; sauté 5 minutes or until tender.
Melt butter in a medium saucepan over medium heat. Stir in flour; cook 2 minutes, stirring constantly with a whisk. Remove from heat; gradually add milk, stirring with a whisk. Return pan to heat; bring to a boil. Cook 6 minutes or until thickened, stirring constantly with a whisk. Remove from heat; stir in black pepper. Add 1/2 cup milk mixture to sausage mixture; stir well.
Preheat oven to 350°.
Spoon about 1/3 cup sausage mixture into each manicotti; arrange manicotti in a single layer in a 13 x 9–inch baking dish coated with cooking spray. Sprinkle mozzarella over manicotti; spread remaining milk mixture evenly over mozzarella. Top milk mixture with pasta sauce, spreading to cover. Sprinkle with Parmesan. Bake at 350° for 35 minutes or until bubbly.