Place onions, garlic and salt in nonreactive soup pot. Cover and cook on medium heat for about 10 mins, stirring often, until the onions are translucent.
Meanwhile, halve and peel the squash, scoop out and discard the seeds, and dice into 1/2 inch cubes. If you have 5 cups or more of cubed squash, increase water by 1/2 to 3/4 cup. Add the squash, jalapeno, cinnamon, cumin, and water to the soup pot and simmer for 5 to 10 minutes. Add the tomatoes and bell peppers and cook for 10 to 15 minutes or until all of the vegetables are tender. Stir in the corn and return to a simmer. Add salt and pepper to taste.
Serve each bowl topped with a dollop of sour cream and a sprinkling of grated cheese.