Preheat oven to 350°F. Spray a baking sheet with cooking spray and set aside. In a large pot, cook the pasta in boiling, salted water until slightly tender but not cooked through (they will finish cooking in the oven). Transfer the pasta from the pot with a slotted spoon to a baking pan to cool, spreading the shells out in a single layer, leaving space between each shell.
Heat the oil in a large pan or pot and add the red chili flakes and garlic. Sauté for about 1 minute, making sure not to brown the garlic, as that will make it bitter. Add the marinara sauce and simmer gently while you make the filling.
In a bowl, combine the spinach, cottage cheese, tofu, 1 cup Parmesan cheese and Italian seasoning; mix thoroughly.
Prepare a 9"x13" glass baking dish by drizzling some marinara sauce on the bottom. Stuff each shell with a rounded tablespoon of the spinach mixture and place into the baking dish. When all the shells are stuffed, pour the remaining sauce over the shells, then sprinkle with ¼ cup of Parmesan cheese.
Bake in the oven for 20 to 25 minutes, until the top is golden brown. Sprinkle the parsley over the top or add a sprig of watercress for color and serve.