Preheat oven to 350 degrees and grease a 9x13-inch baking dish.
Cook and crumble Italian sausage in a large nonstick pan. Once you have it broken apart, add the onion. Cook until the sausage is no longer pink.
Add garlic, Italian seasoning, and crushed red pepper flakes and cook 1 minute.
Turn heat to low and add cream cheese. Stir until melted. Remove from heat.
Let cool slightly and then stir in 3/4 cup of mozzarella cheese, ricotta cheese, and pepper.
Stuff the mixture into the manicotti shells. You can either use a spoon or fork to push it in or you can transfer the mixture ot a large ziptop bag and snip the corner and pipe it in.
Pour about 1/2 cup of sauce in the prepared baking dish and spread it evenly. Place the filled manicotti tubes on top of the sauce.Pour remaining sauce on top of manicotti.
Cover and bake for 25 minutes.
Sprinkle with remaining mozzarella cheese and Parmesan cheese. Bake uncovered for 10 more minutes.