Press the tofu (using either tofu press or by placing it in a shallow bowl, placing a flat plate on top of the tofu, then placing something heavy on top of the plate). Let the tofu sit for 15 minutes and collect excess water in the shallow bowl.
Blend the pressed tofu in a food processor with 1 tablespoon of nutritional yeast, 1 teaspoon of oregano, 1 teaspoon of salt, the garlic powder, lemon juice and 1 tablespoon of oil until smooth and set aside.
Chop the garlic and put in a large pot with a tablespoon of oil. Cook for three minutes on medium high, stirring constantly.
Blend canned tomatoes in a blender until smooth and add them along with basil, thyme, bay leaves, red chile flakes and the remaining oregano, salt, and nutritional yeast to the pot.
Once it reaches a low boil, cover the pot and reduce the heat to simmer for 30 minutes.
Preheat the oven to 350 F and cook the manicotti noodles in separate pot.
Add half of the dairy-free mozzarella to the tofu mixture and stuff the cooked manicotti shells.
Pour about ½ cup of the sauce into a 9x13-inch baking dish.
Place the stuffed manicotti shells into the prepared baking dish.
Top with about 1 cup of the marinara sauce and the remaining cheese.
Bake for 40 minutes. Top with fresh basil, and serve with the extra sauce.