saute onion in oil until tender. add garlic, saute for another minute. add tomatoes, herbs and spices. Add beans, and enough water to cover the beans by about 2 inches. bring to boil. add chipotles to soften. cover and lower heat. Simmer. Remove chipotles when softened about 20 minutes. stem and chop chipotles. toss half of them back into pot. simmer for 2 hours or until beans are tender. If the heat is not hot enough add more chipotles if fine the chipotles will store in refrigerator for 2 days.