Put pasta on to boil, making sure you keep it a little firm, otherwise it’ll start to fall apart when you stir in the cheese sauce.
In a large pot over medium heat, melt the Earth Balance, then add the onions, cooking for about 2 minutes. If you need more moisture, you can add a tablespoon of water or more EB.
Add flour, and mix all together- this is your roux. Cook for another minute.
Pour in veggie stock and squash, stir until completely blended. This is your chance to make sure there are no large chunks of squash swimming around in there! Make sure you’re constantly scraping the sides of the pan, I recommend using a rubber spatula.
Add soy cream and stir, letting it come to a slow bubble, then add the Daiya. Keep stirring (Don’t stop!)
Once it’s all melty and gooey, add in your nutmeg, salt and pepper. Taste and adjust. But don’t taste too much, or there wont be any left! Pour in your (slightly undercooked) pasta, and that’s it!
http://www.thatwasvegan.com/2011/12/12/butternut-squash-mac-n-cheese/