Preheat oven to 350°.
Cook sausage, crumbling as it cooks until well browned. Drain excess grease and set aside.
Meanwhile, In another pan, cook diced onion in olive oil over medium heat until softened, about 5 minutes. Stir in tomato sauce, 2 teaspoons of granulated garlic, 1 teaspoon kosher salt and 1 teaspoon pepper. Cook 10 minutes, stirring often.
Stir in cream and remove from heat.
Bring a pot of water to a boil and cook manicotti in batches, cooking about 6 minutes. Remove from water with tongs and set aside on a sheet pan in a single layer. Pasta will finish cooking in the oven.
Spoon about 1 1/2 cups of sauce into the bottom of a 10 x 15 baking dish.
Mix filling together by combining cooked sausage, ricotta cheese, 1 cup of shredded mozzarella, 1 cup of shredded Parmesan, eggs, 2 teaspoons of granulated garlic, thyme, basil, 1 teaspoon salt and 1 teaspoon pepper.
Use a spoon to stuff shells with filling, laying stuffed shells into baking dish over sauce.
Pour remaining sauce over stuffed shells.
Top with remaining 2 cups of shredded mozzarella.
Bake, uncovered for 40 - 45 minutes.
Remove from oven and allow to rest 10 minutes before serving.