Combine 6 cups water, beans and onion in large pot. Bring to boil. Reduce heat, cover partially and simmer until beans are tender, about 1 hour 20 minutes. Cool in cooking liquid. Drain bean mixture, discarding cooking liquid.
Meanwhile, place chicken in medium bowl. Add 1 tablespoon oil, oregano, thyme and rosemary and toss to coat. Let stand 30 minutes at room temperature.
Heat remaining 1 tablespoon oil in heavy large deep skillet over medium-high heat. Sprinkle chicken with salt and pepper. Working in batches, cook chicken in skillet until golden brown, about 4 minutes per side. Transfer to plate.
Pour off drippings from skillet. Add wine and garlic to skillet; simmer until liquid is reduced by half, scraping up browned bits, about 2 minutes. Stir in squash, tomatoes in juice and drained bean mixture. Season with salt and pepper. Add chicken to skillet. Cover and simmer until chicken is cooked through and squash is tender, about 40 minutes. Stir in parsley. Simmer uncovered until sauce thickens slightly, about 3 minutes. Transfer chicken to serving bowl. Spoon bean-and-vegetable mixture over.
