Preheat oven to 350 degrees F and grease a 9x13 inch baking dish with cooking spray.
Place cottage cheese, 1/2 of the mozzarella, 1/2 of the parmesan, Italian seasoning, basil, garlic powder, onion powder, salt, pepper, and eggs into a food processor.
Process until combined. It's okay if it's still a little chunky. Set aside.
Pour half the sauce into the bottom of prepared pan.
Stuff cooked shells with the cheese mixture (spoon it in or pipe using a ziplock baggie), then place them in prepared baking dish.
Pour on remaining sauce then top with remaining mozzarella and parmesan.
Bake in preheated oven for 30 minutes, until edges are bubbly and shells are slightly set.