Boil the beans and water in a saucepan over high heat. Reduce the heat, cover partially, and simmer 65-75 minutes. Drain.
Preheat the oven to 400�F. Cut the tortillas into wedges and place on a baking sheet. Bake 4-5 minutes until crisp and set aside.
Heat the broiler, positioning the cooking rack 4 inches from the heat source. Line a baking sheet with aluminum foil, and add the tomatoes, yellow onion wedges, and jalape�os. Broil 4-5 minutes, stir the vegetables, and broil 3-4 minutes longer. Transfer to a covered bowl and let cool 10 minutes.
Reduce the oven temperature to 350�F. Peel the tomatoes and jalape�os, then coarsely puree in a blender. Add the cilantro and 1/2 teaspoon of salt, pulsing 1-2 times. Set aside.
Heat 2 1/2 tablespoons of oil in a frying pan over medium-high heat. Saut� the garlic 1-2 minutes, then add the cooked beans and the remaining salt. Cook 3 minutes, then remove from the heat.
Grease a baking dish with the remaining oil. Spread 1/2 cup of tomato sauce in the dish and layer 1/3 of the tortilla wedges and 1/3 of the bean mixture. Repeat the layering, then top with the remaining sauce. Sprinkle with the cheese and bake 25-30 minutes.
Cut into squares, garnish with the green onion, and serve.
