In a large saucepan over high heat, combine the beans, water, bay leaf and 1/2 teaspoon of the salt. Bring to a boil. Reduce the heat to low, cover partially and simmer until the beans are tender but still firm, 60 to 70 minutes. Drain and discard the bay leaf.
When the beans are cooked, coarsely chop the roasted bell peppers and set aside. In a large saucepan, heat the oil over medium heat. Add the yellow onion and saute until soft and lightly golden, about 6 minutes. Stir in the garlic, chili powder, oregano, cumin, red pepper flakes and the remaining 1 teaspoon salt. Cook until fragrant, 1 to 2 minutes. Add the bell peppers, cooked beans, tomatoes and cilantro and cook until the tomatoes are heated through, 5 to 6 minutes. Ladle the chili into individual bowls and sprinkle with the cheese and green onions.