Season the squash with olive oil, salt and pepper. Place on a baking sheet, flesh side up and add 1/2 cup water to the pan. Cover with alluminum foil and bake until tender, about 1 hour. Remove from the oven and cool completely.
In a large saute pan, over medium heat, brown the sausage and onions, about 6 to 8 minutes.
In a large mixing bowl, toss the sausage and onions with the pasta sauce, pasta, and cheese. Season with salt and pepper. Mix well.
Spoon the pasta mixture into the cavity of each squash. Place the filled squashes on a baking sheet and place in the oven.
Bake until the squash is heated through and the cheese melts, about 20 minutes.