Coat chicken with vinegar, annatto paste, salt, cumin, thyme, pepper, and cilantro. Set aside.
In a large pot, heat oil over medium-high heat.
Add brown sugar to pot. Cook until melted and dark brown. Do not burn.
Add garlic and ginger to pot. Once ginger has browned, remove.
Add chicken to pot and sear on all sides.
Add onion, tomato, bell pepper, and half cup of water to pot.
Reduce heat to medium and simmer covered for one hour. Add water as needed to keep chicken moist.