Preheat oven to 350 degrees F. Boil a pot of water and cook manicotti for only a minute. Drain. You basically want to soften them and start the cooking process, but they still need to be extremely firm in order to stuff. They will continue cooking in the oven.
In a large bowl, combine ricotta, garlic, half of the mozzarella, half of the Parmesan, eggs, Italian seasoning, basil, salt and pepper, and red pepper flakes. Mix well. Add to large resealable plastic bag.
Add about ½ cup of the sauce to the bottom of an 11x17 baking dish. Snip the corner off the bag with 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 in preheated oven covered for about 45 minutes. Remove foil and continue cooking until cheese is melted, about 15 additional minutes.
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.