Preheat the oven to 400°F. Place spaghetti squash halves cut-side-down in a glass baking dish. Pour in enough water to come 1-inch up the sides of the dish. Microwave on high for 5-8 minutes, or until the squash is tender and can easily be pierced with a fork. Set aside until cool enough to handle.
Meanwhile, in a large skillet on the stovetop, cook onion in olive oil over medium high heat. Cook for 3-5 minutes until softened.
To the skillet add chicken, marinara sauce, garlic salt, Italian seasoning, black pepper, red pepper flakes.cStir well, remove from heat.
To the pan add 1 cup shredded mozzarella cheese and 2 Tbsp Parmesan cheese plus Italian parsley and basil. Stir until fully incorporated.
Assemble: Turn the squash halves cut-side-up and use a fork to loosen the inside of the spaghetti squash into strands. Scoop spaghetti strands into the skillet with the chicken mixture and stir to combine.
Divide the filling mixture and stuff each squash half with the chicken and spaghetti squash mixture and top with reserved mozzarella and Parmesan cheese.
Place the stuffed squash halves in a baking dish and transfer to the preheated oven. Cook for 20-30 minutes, or until hot and bubbly. You can increase the oven temperature to broil to brown the cheese further, if needed.
Garnish with fresh basil and serve.
**Bake the Squash** You can bake the spaghetti squash in the oven, instead of the microwave. Bake at 375°F for 45-55 minutes, then proceed with the recipe as written.