In a bowl, cover kidney beans with cold water by 2 inches. In a separate bowl, cover remaining beans with cold water by 2 inches. Let soak for at least 6 hours.
Drain and rinse kidney beans, transfer to a pan and cover with fresh water. Bring to a boil and cook for 10 to 15 minutes; drain.
Drain remaining beans and transfer to a slow cooker. Cover and chill 1 cup diced onion. Add sweet potatoes, garlic and chiles to slow cooker. Stir in tomatoes, molasses, cumin, oregano, remaining onion, kidney beans and 3 cups water. Cover and cook on low until beans are tender, 8 to 9 hours.
Uncover, season with salt and pepper and stir. Divide among bowls. Top with chilled onion.