Prepare the pasta using the package directions, omitting the salt. Drain well in a colander.
Meanwhile, in a large nonstick skillet, heat the oil over medium heat, swirling to coat the bottom. Cook the onion for 3 to 4 minutes, or until tender-crisp.
Stir in the squashes, water, and pepper. Cook for 6 to 8 minutes, or until the squashes are tender-crisp, stirring occasionally.
Stir in the beans, tomato, basil, and vinegar. Cook for 3 minutes, or until heated through, stirring occasionally. Stir in the salt.
Serve 1 cup pasta and 1 cup bean and squash mixture
Sprinkle with the Parmesan.