Cook the shells: Boil in salted water until just shy of al dente. Drain and rinse with cool water so they’re easier to handle.
Set aside on a tray.
Prep the filling: In a bowl, stir cottage cheese until slightly creamy. Add 1/2 cup mozzarella, 1/4 cup Parmesan, egg whites, garlic, basil, oregano, red pepper flakes, spinach, and a pinch of salt and pepper. Mix until combined.
Taste and adjust: Add more salt, pepper, or herbs as needed.
The filling should be well-seasoned since the pasta is mild.
Prepare the pan: Lightly oil a 9x13-inch baking dish. Spread 1 cup marinara across the bottom.
Stuff the shells: Spoon about 2 tablespoons of filling into each shell. Nestle stuffed shells into the sauced dish, open side up.
Top and cover: Spoon the remaining marinara over the shells.
Sprinkle with the remaining 1/2 cup mozzarella and 1/4 cup Parmesan.
Bake: Cover with foil and bake at 375°F (190°C) for 20 minutes. Uncover and bake 10–15 minutes more, until bubbly and lightly golden.
Rest and serve: Let stand 5–10 minutes. Garnish with fresh basil or parsley and a crack of black pepper.