Adjust oven rack to middle position and heat oven to 375. Heat oil, garlic, and pepper flakes in large saucepan over medium heat until fragrant but not brown, 1 to 2 minutes. Stir in tomatoes, basil and 1/2 teaspoon salt and simmer until thickened slightly, about 15 minutes. In a medium bowl, combine ricotta, 1 cup Parmesan, mozzarella, eggs, salt, pepper, parsely, and basil; set aside. To assemble, pour 1 inch boiling water (about 4 cups) into 13 by 9-inch baking dish, then add noodles one at a time. Let noodles soak until pliable, about 5 minutes, separating noodles with tip of sharp knife to prevent sticking. Remove noodles from water and place in single layer on clean kitchen towels; discard water in baking dish and dry baking dish. Spread bottom of baking dish evenly with 1 1/2 cups sauce. Using a spoon, spread 1/4 cup cheese mixture evenly onto bottom three-quarters of each noodle (with short side facing you), leaving top quarter of noodle exposed. Roll into tube shape and arrange in baking dish seam side down. You should be able to fit 8 manicotti in each row, allowing all 16 to fit in the dish. Top evenly with remaining sauce, making certain that pasta is completely covered. Cover manicotti with aluminum foil. Bake until bubbling, about 40 minutes, then remove foil. Sprinkle manicotti evenly with remaining 1 cup Parmesan. Bake until cheese is browned and bubbly, about 6-7 minutes. Remove from oven and let sit for 15 minutes before serving. Before baking, cover with a sheet of parchment paper, then wrap in foil. Refrigerate for up to 3 days or freeze for up to 1 month. Remove the parchment and replace the foil. Follow baking directions above, but increase baking time to 60-75 minutes.