Preheat oven to 375 F. Lightly spray a 9x13-inch baking dish with non-stick cooking spray.
Add about 1/2 of the marinara sauce in the bottom of the pan.
Add the cottage cheese, shredded mozzarella cheese, Italian seasoning and salt and pepper into a gallon size FREEZER bag and gently knead until it is mixed up.
Cut a small corner of the bag, about 1/2-inch wide. You want the filling to flow easily through the opening, but you don't want it to pour out too quickly.
Pipe the filling into the manicotti shells, from both sides. Fill all the shells and place into the marinara lined pan.
Cover all the shells with the remaining marinara sauce.
Sprinkle the other mozzarella cheese on top. Cover with foil.
Bake in the preheated oven for 1 hour, and let stand 1 minute before serving.
To freeze before baking: add foil to the top and freeze in the fridge freezer to 6 months, or deep freezer for 12 months.
To thaw and cook: thaw for at least 24 hours in the fridge. Bake as directed.