Heat oven to 375°F. Lightly grease a 9x13-inch baking dish.
Boil shells in salted water until very al dente, 8–9 minutes. Drain and cool.
Warm olive oil in a large skillet over medium heat. Add onion and a pinch of salt.
Cook onion until softened, 3–4 minutes. Stir in garlic and cook 30 seconds.
Add ground beef. Brown, breaking up, until no pink remains. Drain excess fat.
Season beef with Italian seasoning, red pepper, black pepper, and about 1 tsp salt.
Pour in 1 cup marinara. Simmer 2 minutes, then remove from heat to cool slightly.
In a bowl, combine ricotta, 1 cup mozzarella, Parmesan, and half the herbs.
Fold cooled beef mixture into the cheeses until evenly combined.
Stir 1.5 cups marinara with water. Spread in the bottom of the baking dish.
Fill each shell with a heaping spoonful of the beef-ricotta mixture. Arrange in dish.
Spoon remaining marinara over shells. Top with remaining mozzarella.
Cover with foil and bake 20 minutes. Uncover and bake 10–15 minutes until bubbly.
Rest 5 minutes. Finish with remaining herbs and serve warm.