Cook the spaghetti squash in the microwave: wipe the skin clean, pierce it in a few places with a sharp knife, place on a microwave-safe plate and microwave on high for 5 minutes on each side, until tender.
Allow the cooked spaghetti squash to rest 10 minutes, until cool enough to handle. Cut it open with a sharp knife. Use a large spoon to discard the pulp and seeds. Rake a fork back and forth to create spaghetti-like strands, placing the strands in a large mixing bowl. Work carefully so that the shells remain intact, and leave some flesh in the shells.
Add the marinara sauce to the spaghetti squash strands. Mix well to coat. Mix in 2 oz of the mozzarella.
Sprinkle the inside of the spaghetti squash shells with salt and pepper. Transfer the marinara coated strands back into the shells. Arrange the pepperoni on top and sprinkle with the remaining mozzarella and with the Parmesan.
Place the stuffed spaghetti squash shells in a square 8-inch baking dish, or any baking dish that will hold them snugly. Bake until cheese is melted and lightly browned, about 15 minutes.
Remove the spaghetti squash pizza boats from the oven. Sprinkle with parsley. Allow to cool 5 minutes before serving.
*How much marinara sauce you use depends on how low carb you want to keep this dish. I usually use 1/2 cup, but you can go up to 1 cup.