Soak the beans overnight, or for at least 6 hours, in enough cold water to cover. Drain and transfer to a large pot or Dutch oven. Add the water and bay leaves. Bring to a boil, reduce the heat, and simmer, covered, until almost tender, 45 to 50 minutes. Add 1 tablespoon of the salt and cook 10 more minutes.
Make the croutons: Preheat the oven to 350 degrees F. Spread the bread cubes on a baking sheet and bake until golden brown, 5 to 10 minutes. Transfer the cubes to a large bowl and toss with the garlic, salt, pepper, oil, and sage. Let stand 30 minutes.
Meanwhile, heat the oil in a second large pot or Dutch oven over medium heat. Add the onion, carrot, celery, parsnip, garlic, and sage, and cook until the vegetables have softened but are not colored, about 10 minutes. Add the squash and cook for 10 more minutes. Season with the remaining tablespoon of salt, and the black and Aleppo peppers. Remove from the heat and set aside.
Spoon 1 cup of the cooked beans along with 1/4 cup of their cooking liquid into a blender and puree until smooth. Using a rubber spatula, scrape the puree into the pan with the vegetables. Add the whole beans with their cooking liquid, the bay leaves, and honey, and simmer until the vegetables are completely tender, about 10 more minutes. Taste and adjust the seasoning if desired.
Serve the soup in warm bowls, topped with the croutons.
Recipe courtesy of Second Helpings from Union Square Cafe (HarperCollins, 2001) by Danny Meyer and Michael Romano