Long cooking in a covered pot concentrates the sweet, nutty flavor of squash. If the vegetable begins to brown as it cooks, lower the heat and add a splash of water.
In a large pot, heat oil over medium-low. Add onion, squashes, and 2 tablespoons water. Season with salt and pepper, and toss well. Cover, and cook, stirring occasionally, until soft, 30 to 35 minutes.