Chop up onions and mince garlic; set aside. With cleans hands or a mortar and pestle, mash up chipotles with their sauce; set aside. Sauté onions in a large pan until soft, and add to a large pot with garlic and spices. Stir in tomato sauce and chipotle peppers, broth, beer, water, and beans. Heat to a boil, stirring occasionally. Reduce heat to a simmer and then cook uncovered for an hour. Add chicken at the end.