Sort and wash beans; place in a large bowl. Cover with water to 2 inches above beans; cover and let stand 8 hours or overnight. Drain.
Place wheat berries in a medium bowl; cover with water to 2 inches above wheat berries. Cover and let stand 8 hours or overnight. Drain. Place wheat berries in a large saucepan. Cover with water to 2 inches above wheat berries. Bring to a boil; reduce heat, and simmer 25 minutes. Stir in 1/2 teaspoon salt; cook 20 minutes or until tender. Drain.
While wheat berries are cooking, heat oil in a Dutch oven over medium heat. Add the onion, celery, carrot, 1 tablespoon fresh rosemary, and 3 crushed garlic cloves, and cook 12 minutes, stirring occasionally. Stir in beans, 8 cups water, parsley sprigs, thyme sprigs, and bay leaf. Partially cover, and cook 1 1/2 hours or until beans are tender. Discard bay leaf, parsley, and thyme. Stir in wheat berries, 1/2 teaspoon salt, 1/4 teaspoon pepper, and tomatoes; cook 5 minutes or until thoroughly heated.
To prepare garnish, combine chopped parsley, cheese, 1 tablespoon fresh rosemary, 1/4 teaspoon pepper, and chopped garlic. Ladle soup into bowls; sprinkle each serving with about 2 tablespoons garnish.
Note: Wheat berries can be found in most health-food stores and many larger supermarkets.