Cook the squash: Preheat oven to 400 degrees F. Wash squash and carefully cut a thin slice off the bottom (non-stem end) of each squash. Using a large chef’s knife, cut each squash in half starting from bottom and cutting through stem side. (This is best done by placing the knife in the flesh of the squash then giving a good, firm whack of knife+squash on the cutting board or counter.) Scoop out and discard seeds from each squash half. Place flesh-side down, in an 8x11 inch glass baking dish. Add about an inch of water to the pan, cover with foil and bake 1 hour (about 30 minutes for kabocha; it cooks faster than most).
Heat butter in large soup pot or dutch oven. Add onions and jalapeno and cook, covered on low heat for 10 – 15 minutes until onions are soft, but not browned. Scoop flesh from cooked squash halves and add to the onions. (Be careful not to scoop any of the tough skin. If you accidentally do, remove it and discard.) Add chicken broth, cumin and salt and simmer gently for 30 minutes then remove pot from heat. Using a hand-held immersion blender, purée the soup. Garnish as you like and enjoy!