Cut squash in half lengthwise; discard seeds. Place squash cut side down in a 15x10x1-in. baking pan; add 1/2 in. of hot water. Bake, uncovered, at 350° for 30-40 minutes. Drain water from pan; turn squash cut side up. Bake 5 minutes longer or until squash is tender.
Meanwhile, in a nonstick skillet, bring water to a boil over medium heat; add pepper and onions. Cook and stir for 2 minutes. Stir in the tomatoes, parsley, dill, basil and salt. Bring to a boil. Reduce heat; simmer, uncovered, for 5 minutes or until tender.
When squash is cool enough to handle, scoop out pulp, separating strands with a fork; place in a large bowl. Add tomato mixture and toss to combine. Sprinkle with cheese.