Preheat the oven to 375°F (190°C). Pour one jar of marinara into the bottom of each of two 9x13-inch baking dishes.
Bring a large pot of salted water to a boil. Cook the pasta shells for about 8 minutes until al dente, then drain and rinse under cold water; set aside to drain thoroughly.
In a large bowl, combine the cottage cheese, 1 cup of the grated mozzarella, Parmigiano Reggiano, eggs, dried oregano, dried basil, and salt and pepper to taste. Stir until evenly mixed.
Transfer the filling to a disposable piping bag or a large freezer bag and snip a 1-inch hole in the corner; alternatively, use a spoon. Fill each shell with the cheese mixture.
Arrange the filled shells in the prepared pans, placing about 20 shells per pan in a single layer.
Spoon the Alfredo sauce evenly over the filled shells (spread between the two pans). Sprinkle the remaining 1 cup of mozzarella over the tops (about 1/2 cup per pan).
Cover both pans tightly with aluminum foil sprayed with nonstick cooking spray and bake for 30 minutes. Remove the foil and bake uncovered for an additional 15 minutes to brown the tops.
Alternatively, keep pans covered for the full 45 minutes and then broil briefly if you want browned tops.
Remove from the oven and let the shells rest 5–10 minutes. Sprinkle with chopped fresh parsley if using, then serve hot.