Cook shells as per the package instructions, three minutes less than that directed on the packet. Drain, rinse with cold water, drizzle olive oil, and toss to coat the shells. Preheat the oven to 350° F.
In a medium bowl, combine ricotta cheese, 1 cup shredded mozzarella cheese, 1/2 cup grated Parmesan cheese, egg, minced garlic, fresh parsley, 2 tablespoons fresh basil, dried oregano, red pepper flakes (optional), ground nutmeg, salt, freshly cracked black pepper. Mix until well incorporated.
Spread 1 cup of marinara sauce in the bottom of the baking dish. Stuff the shells with a spoon or a pastry bag, about 2 tablespoons per shell. Place the stuffed shell, seam side up, on top of the sauce. Repeat with the rest of the shells.
Top the shells with the rest of the marinara sauce, sprinkle the remaining 1 tablespoons of chopped basil, remaining 1 cup of shredded mozzarella cheese, and1/4 cup of grated parmesan cheese.
Cover the baking dish with aluminum foil, and bake at 350° F for 30-35 minutes. Uncover and bake for another 5-10 minutes, until the sauce begins to bubble and the cheese has melted.
Let the baked shells rest for 5-10 minutes, sprinkle some chopped parsley, and serve. Enjoy!