Wash beans; place into a 6-quart stockpot with water to cover and let soak for 8 hours.
Rinse and drain beans. Bring drained beans, 3 quarts water, and chicken bouillon to a boil in the pot over high heat. Cover, reduce heat to low, and simmer for 3 hours. Do not drain.
Blend onion and bell pepper in a food processor until smooth.
Heat oil in a large skillet over medium-high heat. Saute garlic in the hot oil for 1 minute. Add onion mixture and cook, stirring constantly, for 4 minutes. Stir mixture into beans. Add sugar, oregano, cumin, salt, and pepper. Let simmer, uncovered, until beans are tender and soup is thickened, 1 1/2 to 2 hours. Garnish with minced onion.