Cook onion, bell pepper and jalapeno for 5-6 minutes until softened.
Add soaked beans, broth, sauteed veggies, garlic, tomato paste, and seasonings. Hold vinegar, sugar, and tomatoes for later.
Cook Low: 6-8 hours
In the last 30-60 minutes, stir in tomatoes. When done, stir in vinegar, sugar, and liquid smoke. Adjust salt/pepper to taste