Heat a large skillet over medium-high heat. Cook and stir beef, onion, and roasted garlic in the hot skillet until browned and crumbly, 5 to 7 minutes. Continue to simmer until pan juices evaporate, about 10 minutes more. Add diced tomatoes, tomato paste, sugar, 1 1/2 teaspoons salt, oregano, thyme, bay leaf, 1/2 teaspoon pepper, and garlic salt; bring to a boil. Reduce heat to medium-low and simmer until flavors blend, about 30 minutes.

Preheat oven to 350 degrees F (175 degrees C).

Bring a large pot of lightly salted water to a boil. Cook manicotti in the boiling water, stirring occasionally until cooked through but firm to the bite, about 8 minutes. Drain and cool slightly.

Mix mozzarella cheese, cottage cheese, 1/4 cup Parmesan cheese, egg, 1/2 teaspoon salt, and 1/2 teaspoon pepper in a bowl. Spoon a generous amount of the cheese mixture into each manicotti shell.

Pour enough tomato-beef sauce to cover the bottom of a 9x13-inch baking dish. Arrange stuffed manicotti over sauce; pour remaining sauce over pasta. Cover with aluminum foil.

Bake in the preheated oven until bubbly, about 30 minutes. Sprinkle remaining 1/4 cup Parmesan cheese over manicotti and return to the oven. Bake until cheese filling is melted, 10 to 15 minutes more.