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 microwave-safe plastic wrap. Microwave on 100% power (high) 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 onion and garlic; cook about 5 minutes or until tender. Stir in tomatoes, tomato sauce, Italian seasoning, salt, fennel seeds, and pepper. Bring to boiling; reduce heat. Simmer, uncovered, for 15 to 20 minutes or until sauce reaches desired consistency, stirring frequently.
Using a fork, remove the squash pulp from shells. Place squash pulp in a colander set in the sink and press with a spatula to remove any excess moisture. Spoon drained squash onto individual plates; top with marinara sauce. If desired, sprinkle with Parmesan cheese and oregano.