Preheat oven to 375°F. Line a rimmed baking sheet pan with heavy duty foil and spray with cooking spray.
Cut spaghetti squash in half from top to bottom. Use a spoon to scrap out the seeds and pulp. Season with salt and pepper to taste. Place cut side down on the sheet pan. Bake for 55-70 minutes or until a knife easily pierces the center.
Meanwhile, In a large heavy bottomed pot or Dutch oven, cook onion and Italian sausage in a drizzle of olive oil over medium-high heat. Cook for 6-8 minutes or just until no pink remains. Drian excess fat from the pot. Add the garlic, cook for 1-2 minutes longer.
To the pot add crushed tomatoes, diced tomatoes, tomato sauce, garlic salt, Italian seasoning, black pepper and crushed red pepper flakes. Stir to combine. Bring the sauce mixture to a gentle boil then immediately lower the heat to medium low. Cover and let simmer for 25-30 minutes stirring occasionally.
Once sauce is done, uncover and add the tomato paste and 4 Tbsp Parmesan cheese. Stir to combine until the tomato paste has melted. Simmer uncovered for 10 minutes. Remove from the heat.
Use a fork to shred the spaghetti squash into long strands. Place into a colander lined with paper towels. Take another doubled paper towel and gently press excess liquid from the squash. Don't mash, just gently blot, then fluff the squash with a fork.
Assemble: Spray a 9x9-inch or 10-inch oblong baking dish with cooking spray. Ladle 1 cup of the sauce on the bottom. Top with 1/2 of the spaghetti squash. Spread the squash with 1 cup sauce and then cover with 1 cup mozzarella cheese.
Spread 1 cup sauce over the mozzarella cheese, then top with final half of Spaghetti squash. Drizzle the final layer of spaghetti squash with 1 cup of sauce. Cover the top with reserved 1 cup mozzarella cheese. Sprinkle with 2 Tbsp Parmesan cheese.
Bake in the 375°F oven for 25-30 minutes until the bubbly and the cheese is golden brown.
Let stand 5 minutes, then cut with a knife into portions and serve. (Drain any excess liquid carefully from the dish, if needed.)