Preheat the oven to 375°F (190°C).
Bring a large pot of salted water to a boil and cook the pasta shells for about 8 minutes until al dente; drain, rinse with cold water, and let them drain thoroughly.
Pour the marinara sauce into the bottoms of two 9×13-inch baking dishes, dividing it evenly between the pans (one jar per pan).
In a large bowl, combine the cottage cheese, 1 cup grated mozzarella, Parmigiano Reggiano, eggs, dried oregano, dried basil, and salt and pepper to taste; stir until well mixed.
Fill a piping bag or a large freezer bag fitted with a 1-inch hole (or use a spoon) and pipe or spoon the cheese mixture into each shell until filled.
Arrange the filled shells in the prepared baking dishes, placing about 20 shells in each pan.
Spoon the Alfredo sauce over the filled shells, then sprinkle the remaining 1 cup of grated mozzarella evenly over both pans (about 1/2 cup per pan).
Cover each pan with aluminum foil (spray the underside with nonstick spray if desired) and bake for 30 minutes; remove the foil and bake uncovered for an additional 15 minutes to brown the tops.
Let the dishes rest for 5–10 minutes after baking, sprinkle with chopped parsley if using, and serve hot.
