Cook macaroni according to package directions; drain well.
Place ricotta and cream cheese in a bowl and mash together. Stir in 1 cup shredded cheese, egg, chopped basil and garlic. Season with salt, pepper and nutmeg; set aside.
Preheat oven to 400 degrees F.
In large pot of boiling water, cook pasta until al dente, or barely tender. Drain well, making sure to empty shells of any remaining water; set aside to cool briefly.
Spread about 1/2 cup marinara sauce over bottom of large baking dish. Spoon ricotta mixture evenly into shells and arrange in dish. Pour remaining sauce over top. Cover with aluminum foil and bake for 30 minutes. Uncover dish, sprinkle with remaining shredded cheese and bake for an additional 10 minutes.