Cut the spaghetti squash in half and remove the seeds. Place in a covered dish with ¼ inch of water and microwave for 10 -12 minutes. In a medium sized skillet over medium heat, add the butter, onions, red pepper, garlic salt, salt, and pepper and cook until the onions are brown in color.
Using a fork, scrape the insides of the squash and transfer to a small bowl. Mix the squash, onions, sour cream, and half the cheese together and mix well. Transfer the mixture to a buttered baking dish and top with remaining cheese.
Bake at 375º for 20-25 minutes. Put on broil in the last minute until golden brown on top.