Make The Sauce:
In a large saucepan, heat the oil (2 tablespoons) over medium heat until it begins to shimmer. Add the onion (1 ½ cups), salt (¾ teaspoon), and pepper (½ teaspoon) and sauté until the onion is translucent about 10-12 minutes. Add garlic (1 tablespoon) and continue to sauté until fragrant, about 1 minute.
Add the crushed tomatoes (1 can), water (2 cups), rosemary (1 teaspoon), Italian seasoning (2 teaspoons), and sugar (1 teaspoon) to the saucepan and bring to a boil. Immediately lower heat to low and cook uncovered until flavors have melded about 10 minutes.
Preheat oven to 400°F.
Make The Filling:
In a mixing bowl, stir together all the filling ingredients until smooth and well combined.
Place the uncooked jumbo shells (25 to 30) on your workspace, open side up. Use a spoon or a pastry bag to fill the shells.
Assembly:
Add 1 cup of the sauce evenly over the bottom of the 9×13-inch baking dish.
Place the stuffed shells, open side up, in the baking dish.
Pour the remaining sauce evenly over the shells. They will be completely covered.
Place aluminum foil, tightly over the baking dish. Bake in preheated oven until shells are tender and the sauce is boiling rapidly about 45-55 minutes. Remove dish from oven. Take off the foil and discard.
Sprinkle the remaining mozzarella evenly over the top of the shells, return uncovered to the oven, and continue to bake until the cheese is melted and beginning to brown, about 15 minutes. Remove from oven and allow the dish to sit for 15 minutes before serving. Sprinkle top with parsley of basil and serve.