Preheat oven to 375F and line a 9x13 casserole dish with 1.5 cups of marinara sauce.
Cook shells in a pot of salty water according to package until al dente - slightly less cook time than fully cooked because they will continue to cook in the oven. Drain and set aside.
Saute onion in olive oil over medium-high heat for 3-4 minutes. Add in turkey sausage and as it cooks, break apart into fine pieces. Cook until no longer pink and fully cooked through. Set aside to cool for 10 minutes.
In a large bowl, mix together cottage cheese, ½ cup parmesan cheese, spinach, parsley, ½ cup pesto, garlic, oregano, red pepper flake, salt, and pepper. Add in the turkey sausage mixture and mix until all combined.
Individually stuff each shell with a good amount of mixture - about ¼ cup and then lay each shell down in the sauced casserole dish. Repeat until all shells and mixture are finished.
Pour remaining 1.5 cups marinara sauce over top of shells, along with spooning on remaining ½ cup of pesto throughout the top. Then top with mozzarella cheese and remaining ½ cup parmesan cheese.
Bake covered with foil for 20 minutes, then remove cover and bake for additional 10 minutes.
Sprinkle with remaining parsley and let cool about 15 minutes before serving. Enjoy!