Cook the shells: Boil in well-salted water until just shy of al dente (about 1–2 minutes less than package).
Drain and toss with a little olive oil so they don’t stick. Set aside to cool.
Brown the sausage: In a large skillet over medium heat, warm 1 tablespoon olive oil. Add onion and cook 3–4 minutes until softened.
Stir in garlic for 30 seconds. Add sausage, breaking it up, and cook until browned. Drain excess fat.
Wilt the spinach: Add chopped spinach to the skillet with the sausage.
Cook 1–2 minutes until wilted (or stir in well-drained thawed spinach). Season with a pinch of salt and pepper. Let the mixture cool slightly.
Mix the filling: In a bowl, combine ricotta, 1 cup mozzarella, Parmesan, egg, Italian seasoning, a pinch of red pepper flakes, 1/2 teaspoon salt, and a few grinds of black pepper.
Fold in the cooled sausage-spinach mixture.
Prep the baking dish: Spread 1 to 1 1/2 cups marinara over the bottom of a 9x13-inch dish.
Stuff the shells: Fill each shell with 2–3 tablespoons of the ricotta-sausage mixture. Nestle them seam-side up into the sauce-lined dish.
Add sauce and cheese: Spoon remaining marinara over the shells. Top with the remaining mozzarella and a sprinkle of Parmesan.
Bake: Cover loosely with foil (tent to prevent sticking) and bake at 375°F (190°C) for 20 minutes.
Uncover and bake another 10–15 minutes until bubbling and golden in spots.
Rest and serve: Let sit 5–10 minutes to set. Garnish with chopped basil or parsley. Serve hot with extra Parmesan.