In a large pot, over medium-high heat, heat olive oil, add onions, sugar, salt, garlic, oregano, and thyme. Let the mixture sweat for approximately 10 minutes or until the onions have no resistance to the edge of a spoon.
Add the two cans of crushed tomatoes and let simmer over medium heat. Stir occasionally.
In a large skillet over medium to high heat, cook the sausage, and add the 1/2 chopped onion and 1/2 tablespoon of roasted garlic. Separate the meat as it cooks and allow to cook until there is no more pink.
When the sausage is done, mix into the finished homemade marinara sauce. Stir to combine.
Cook the penne pasta according to package instructions.
Preheat the oven to 375F. Grease a 9 X 13 baking pan and set aside.
In a large bowl (very large bowl), combine cooked penne pasta, sausage and sauce mixture, 1 tablespoon garlic, oregano, basil, parsley, ricotta cheese, 1 cup of mozzarella, parmesan cheese, and egg. Mix together until combined well.
Pour the mixture into the 9 x 13 baking pan and spread the remaining 1/2 cup mozzarella cheese over the top. Bake for 30 minutes.
Notes:
Sauce: If you choose not to make the homemade marinara sauce, you can simply replace with two 32 ounces cans of marinara sauce. The sauce does not need to be warmed up, you simply need to just mix it in with the rest of the ingredients.
Gluten Free: Can be made gluten free simply by using gluten free pasta.
Meal Prep: Can be made ahead and frozen. Simply follow instructions up until it says to bake it in the oven. Don't bake, put it in the freezer and let thaw completely when you are ready to make. When it is thawed, put in the oven for 30 minutes at 375F.
Vegetarian: Make without the sausage.