Cut the spaghetti squash in half and remove the seeds. Place in a covered dish with a 1/4 inch of water and microwave for 10 to 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.
Place into a 375 oven for 20 to 25 minutes. Broil for last minute.
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