Half the squash and then cut into 1/4 inch half moon slices. Preheat oven to 350 degrees.
In a large deep skillet, heat the oil on medium high. Saute the squashes and onion for 3-5 minutes. Add the water, salt, cumin and pepper flakes. Saute until the skin of the squash are still crisp and just starting to turn translucent. Add the ketchup, 1 cup of the chips and 1 cup of cheese, stirring quickly. Remove from heat to finish combining. Pour into a greased 9x13 inch dish. Top with remaining chips and cheese. Bake for 15-20 minutes.