Heat a large skillet over medium-high heat. Add beef, onion, and roasted garlic; cook and stir until beef is browned and crumbly, about 5 to 7 minutes. Continue simmering until pan juices evaporate, about 10 minutes. Add diced tomatoes, tomato paste, sugar, salt, bay leaf, oregano, thyme, black pepper, and garlic salt; bring to a boil. Reduce heat to medium-low and simmer until flavors blend, about 30 minutes.

Preheat the oven to 350°F (175°C).

Fill a large pot with lightly salted water and bring to a boil. Add manicotti and return to a boil. Cook manicotti, uncovered, stirring occasionally, until tender yet firm to the bite, about 8 minutes. Drain and cool slightly.

Combine cottage cheese, mozzarella cheese, 1/4 cup Parmesan cheese, egg, salt, and black pepper in a bowl. Spoon a generous amount of the cheese filling into each manicotti shell.

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