Partially boil manicotti: Boil a large pot of salted water and cook 5 1/2 ounces manicotti pasta for only a minute. Drain. The goal is to soften the pasta and start the cooking process, but the pasta needs to still be extremely firm in order to stuff. The pasta will finish cooking in the oven.
Prepare cheese filling: In a large bowl, combine 1 pint whole milk ricotta cheese, 4 cloves garlic, half of the mozzarella, half of the Parmesan, 2 eggs, 1 tablespoon dried Italian seasoning, 8 leaves fresh basil, 1/2 teaspoon salt, 1/2 teaspoon pepper, and 1/4 teaspoon red pepper flakes. Mix well. Add to large resealable plastic bag.
Prepare manicotti: Add about 1/2 cup of the sauce to the bottom of an 11x17 baking dish. Snip the corner off the bag containing the cheese filling and pipe it into each manicotti tube. Arrange each tube in the pan on the sauce. Pour remaining sauce on top and sprinkle with remaining cheese. Cover with foil.
Bake: Place manicotti in preheated oven and bake, covered, for about 45 minutes. Remove foil and continue cooking until cheese is melted, about 15 additional minutes.
Notes
This recipe can be made ahead. Do full preparation up to the point where the dish goes in the oven. Keep in the refrigerator, covered. When ready to bake, bring to room temperature prior to baking. Alternatively, manicotti can be taken right from the refrigerator and baked, but baking time (covered with foil) will need to be extended by about 15 minutes.