Preheat oven to 350°. In a large pot of salted boiling water, cook pasta shells until al dente. Drain, then return to pot and let cool.
Meanwhile, make meatballs: In a large bowl, combine ground turkey, bread crumbs, Parmesan, garlic, parsley, and red pepper flakes and season with salt and pepper. Bake until golden brown and cooked through, 10 to 12 minutes.
In a large bowl, stir together ricotta, mozzarella, and spinach and season with salt and pepper.
Pour 1/4 cup marinara in bottom of oven-proof skillet or baking dish. Stuff shells with ricotta mixture and meatballs and arrange in dish, then spoon over remaining marinara.
Bake until shells are hot and bubbly, 18 to 20 minutes.