Preheat oven to 375°F. Spread 1 cup marinara mixed with 1/2 cup water across the bottom of a 9x13 baking dish.
Cook shells in heavily salted boiling water 2 minutes less than package time. Drain and lay flat in a single layer on oiled parchment to cool.
Mix ricotta, 1 cup mozzarella, parmesan, egg, garlic, Italian seasoning, onion powder, nutmeg, salt, and pepper until combined. Fold in spinach if using.
Fill each shell with about 2 heaping tablespoons of filling using a spoon or piping bag. Arrange open side up in the baking dish over the sauce layer.
Pour remaining marinara over the shells. Top with remaining 1/2 cup mozzarella. Cover tightly with foil and bake 30 minutes. Remove foil and bake 10 to 15 more minutes until golden and bubbly. Rest 5 minutes, then garnish with fresh basil and serve.