Preheat the oven to 375 degrees F (190 degrees C). Lightly grease a 9x13-inch baking dish.

Bring a large pot of water to a boil. Add 1 tablespoon kosher salt to the boiling water and stir in pasta. Cook until just about tender to the bite, about 8 minutes (or 1 to 2 minutes less than package instructions).

At the same time, heat a large, deep skillet or saucepan over medium-high heat. Add sausage and beef and cook, crumbling with the back of a spoon, until browned, about 5 minutes. Add onion, garlic, ¾ teaspoon salt, ½ teaspoon pepper, and pepper flakes; cook until onion is translucent and softened, 3 to 5 minutes.

Drain pasta and return to the pot. Add about ½ cup marinara; toss to coat and let sit until needed.

Add remaining marinara sauce to the browned meat mixture. Pour ¼ cup water into each jar, shake to release any leftover sauce in the jar, and pour into the skillet. Stir and bring to a simmer. Reduce heat to medium-low and cook, stirring occasionally, for 10 minutes.

Stir ricotta cheese, ½ cup Parmesan cheese, egg, parsley, basil, and remaining ¼ teaspoon each salt and pepper together in a bowl.

Add 2 cups meat sauce to the pasta; toss to coat.

Spread ½ cup meat sauce into the bottom of the prepared baking dish. Add ½ of the pasta mixture and top with 2 cups meat sauce. Lightly dollop and spread ricotta mixture over the top and sprinkle evenly with 1 ½ cups mozzarella cheese. Add remaining pasta mixture, remaining meat sauce, and remaining mozzarella on top. Sprinkle evenly with remaining ¼ cup Parmesan.

Bake in the preheated oven until golden and bubbly, 25 to 30 minutes. Let stand 10 minutes before serving.