To make the sauce:

1. In a large saucepan over medium heat, heat oil, garlic, and pepper flakes until fragrant but not brown, 1–2 minutes
2. Stir in tomatoes, basil, parsley, and ½ teaspoon salt; simmer until thickened slightly, about 15 minutes.

To make the filling:

1. In a medium bowl, combine ricotta, 1 cup Parmesan cheese, mozzarella cheese, eggs, parsley, basil, salt, and pepper; stir until thoroughly combined.

To assemble and bake:

1. Add 1 inch of boiling water to a 9-by-13-inch baking dish. Add noodles one at a time, soaking until pliable, about 5 minutes. If noodles stick together, separate with the tip of a sharp knife. 
2. Remove noodles from water and place in single layer on clean kitchen towels; discard water.
3. In a dry 9-by-13-inch baking dish, evenly spread 1½ cups sauce along the bottom.
4. With the short side of the noodles facing you, top each with ¼ cup of the cheese filling. Evenly coat ¾ of each noodle, leaving the top quarter exposed. 
5. Roll each noodle into a tube and arrange in two rows of eight in the baking dish, seam side down. 
6. Top evenly with remaining sauce.
7. Place the temperature probe into one of the manicotti in the center of the dish, making sure the tip of the probe is centered in the manicotti. 
8. Place the dish in the cold oven on rack position “3.” Plug the temperature probe into the receptacle. 
9. Select Gourmet Mode and choose One Dish Meals, Casserole, and One Rack. 
10. Bake for 20 minutes then evenly sprinkle remaining 1 cup of Parmesan cheese over the manicotti. Bake until cheese is browned and bubbly, and the probe temperature is reached. Remove from oven and let cool slightly before serving.