At least one day ahead, cover the achiote seeds with 1/4 cup water and bring to a boil. Soak overnight.
With a mortar and pestle or spice grinder, grind the seasonings together and then grind in the seeds with their liquid, orange juice, and vinegar.
Trim excess fat from the chicken and remove the skin. Spread with the achiote paste. Reserve about 1 tbsp to finish the sauce. If available, wrap in banana leaves.
In a medium-size skillet, sauté the tomatoes with onion in hot oil until the onion is soft and translucent, about 8 minutes.
Stir in the reserved achiote paste and pour over the chicken. Cover with foil and bake 50 minutes to 1 hour at 350°.
To serve, transfer the chicken in the banana leaves to a platter. Return the sauce to a skillet and bring to a boil. Spoon over the chicken. Garnish with fresh herbs, such as parsley, cilantro, or watercress, and radish roses.