Cut squash in half lengthwise; remove and discard seeds. Place one squash half, cut side down, in a 2-quart rectangular microwave-safe baking dish; add 1/4 cup of the water. Cover with vented plastic wrap. Microwave about 10 minutes or until tender. Remove squash half; keep warm. Repeat with the remaining squash half and the remaining 1/4 cup water.
Meanwhile, for marinara sauce, in a medium saucepan heat oil over medium heat. Add mushrooms, onion, and garlic; cook about 7 minutes or until tender. Stir in the next six ingredients (through pepper). Bring to boiling; reduce heat. Simmer, uncovered, 15 to 20 minutes or until sauce reaches desired consistency, stirring frequently.
Use a fork to shred and separate the squash pulp into strands. Place squash pulp in a colander set in the sink; press pulp with a spatula to remove any excess moisture. Fluff drained squash with a fork. Spoon squash onto plates; top with sauce. If desired, sprinkle with Parmesan cheese.