Preheat the oven to 375º F.
Cut the squash lengthwise. Remove the seeds with a spoon.
Spray the squash with non-stick spray and place it cut side down on a large baking sheet lined with foil. Bake for 35-40 minutes, or until a knife inserted in the fattest part of the squash can pierce through all of the flesh easily.
While the squash is baking, brown the sausage in a large skillet over medium-high heat.
Using a slotted spoon, remove the sausage from the pan and put it in a small bowl and drain off most of the oil from the skillet (save a little to sauté the vegetables though) then add green and red bell peppers, mushrooms, onion and garlic and sauté until softened. Stir in salt, black pepper and crushed red pepper. Add the sausage back to the skillet and mix all together.
Once the baked squash is cool enough to handle, scoop out a little of the centers (to make space for the filling). Spoon in the filling and top with half of the cheeses. Repeat with the other half of the squash.
Bake the stuffed squash for another 15-20 minutes, or until the cheese is melted and starting to brown.