Cut both spaghetti squash in half lengthwise and scrape out the seeds. Oil the halves and season with salt and pepper.
Place on a cookie sheet and bake for about 30 minutes or until soft.
While the squash bakes, prepare the filling. Place the sausage in a skillet over medium heat. Use a wooden spoon to break up the meat. Once cooked, remove from pan.
Dice the onion and peppers and add to the pan. Saute until the veggies are soft.
Mince garlic and add to the pan with veggies, cook for 1 minute. Add the meat, marinara and salt. Stir well and remove from the heat.
When the squash is done, use a fork to fluff up the squash. It will flake apart and look like spaghetti! Top with the filling; divide among the squash halves and top with shredded cheese.
Broil in the oven until the cheese is melted, about 2 minutes.