Adjust oven rack to middle position and heat oven to 375 degrees.
Cook manicotti shells according to package.
For the sauce, heat oil, garlic and pepper flakes in large saucepan over medium heat until fragrant but not brown, 1-2 minutes. Stir in tomatoes, basil and salt and simmer until thickened slightly, about 15-20 minutes.
In a medium bowl, combine ricotta, 1 cup Parmesan chese, mozzarella cheese, eggs, salt, pepper and herbs.
Spread bottom of 9x13 inch baking dish evenly with 1 1/2 cups sauce.
Stuff each cooked and cooled manicotti shell with ricotta mixture; line up in pan.
Top evenly with remaining sauce, making certain that pasta is completely covered.
Cover manicotti with aluminum foil. Bake until bubbling, about 50 minutes.
Remove foil. Sprinkle manicotti evenly with remaining 1 cup Parmesan. Bake until cheese is browned and bubbly, about 10 minutes.
Remove from oven and let sit for 15 minutes before serving.
NOTE: The manicotti can be prepared right up until the baking step then covered with a sheet of parchment paper, wrapped in aluminum foil, and refrigerated for up to 3 days or frozen for up to 1 month. If frozen, thaw the manicotti in the refrigerator for 1-2 days. To bake, remove the parchment, replace the aluminum foil, and increase baking time to 1 to 1 1/4 hours.