Cook pasta according to package instructions. Using a slotted spoon, transfer the boiled manicotti to cool on a piece of wax paper or foil that has been lightly sprayed with nonstick cooking spray.
Move oven rack to middle position and preheat oven to 375 degrees F.
Pulse 1 can of tomatoes, with their juice, in a food processor until coarsely chopped, about 3 or 4 pulses. Transfer tomatoes to a bowl and repeat with the remaining can of tomatoes.
In a large saucepan over medium heat, add oil, garlic, and red pepper flakes. Heat until the garlic is fragrant, about 1 minute.
Stir in tomatoes and ½ teaspoon of salt and bring the sauce to a simmer. Continue to simmer until the sauce is slightly thickened, about 15 minutes. Stir in fresh basil and season the sauce with salt.
MAKE CHEESE FILLING:
In a medium bowl, stir together ricotta, 2 cups mozzarella, 1 cup of grated Parmesan, eggs, and salt and pepper. Combine ricotta, 1 cup Parmesan, mozzarella, eggs, basil, parsley, and salt and pepper; set aside.
In a 9x13-inch baking dish, spread 1 ½ cups of sauce on the bottom.
Using a spoon, spoon the cheese filling into a cooled manicotti and arrange in baking dish. Repeat with remaining manicotti.
Next, completely cover manicotti with remaining sauce.
BAKE AND BROIL:
Cover baking dish with foil and bake for 40 minutes, or until bubbling.
Remove baking dish from the oven, and adjust the oven rack to the highest position. Close oven and preheat the broiler.
Top manicotti evenly with 1 cup of grated Parmesan cheese and 1/2 cup of shredded mozzarella cheese.
Place manicotti under the broiler and keep a watchful eye as the cheese broils for about 2-4 minutes. Remove the manicotti from the oven once the cheese is melted and is spotty brown.
Cool manicotti for 15 minutes.
Garnish with chopped fresh basil and parsley and serve with additional Parmesan cheese.