Heat the oil in a medium saucepan, with a tight-fitting lid, over medium-high heat. Add the onion, pepper, and annatto, and cook, stirring, until somewhat soft, about 2 minutes. Add the rice and cook, stirring, until toasted, about 2 minutes more. Add water, salt, and bay leaf and bring to a boil. Wrap the lid tightly with a kitchen towel. Cover the rice, lower the heat to a simmer, cook for 20 minutes.
Remove the rice from the heat and set aside, covered, for 10 minutes. Remove the lid and fluff the rice with a fork. Serve with the black beans.
Put the beans in a large saucepan, add the water and bay leaf, and bring to a boil. Set aside, covered, for 1 hour.
Return the beans to a boil, lower the heat to a simmer, cook uncovered, for 1 1/2 hours.
Heat the oil in a medium skillet over medium-high heat. Add the onion and peppers and cook, stirring, until soft, about 5 minutes. Add the garlic, cumin, oregano, and coriander and cook, stirring, until fragrant, about 1 minute more. Add the onion mixture to the beans and continue simmering until the beans are very tender and the liquid has thickened, about 1 1/2 hours more.
If the beans seem too thick, adjust the consistency with a little bit of water. Stir in the vinegar, season with the salt, cayenne, and pepper to taste. Serve.