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In a large saucepan cook, the soaked beans in a lot of water, about 30 minutes or until the beans are tender. Set aside.
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In a large saucepan over medium heat, add oil, cumin seeds and cook for about 3 minutes. Add chopped onions, cook until fragrant and translucent, about 3 minutes. Add annatto, jalapeno, garlic, peppers and cook stirring occasionally for about 5 to 8 minutes. Season with salt and pepper to taste.
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Add tomatoes and juice, bay leaves and the cooked beans. Lower heat and simmer for about 15 minutes, covered. Adjust the salt and pepper if necessary.
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Serve with rice and top with chopped cilantro.