Preheat the oven to 375 F. (If you plan on baking it immediately.)
Dice the onion into small pieces and saute it in 2 tablespoons of oil and 1/2 teaspoon of salt, and 1 teaspoon of thyme, and 2 cloves of minced garlic over low heat for 5 minutes in a large wok.
While the onions are cooking, thinly slice 8 cups of squash into rounds and add them to the onions and stir well and cook for about 10 minutes until the squash has started to soften.
Stir in 1 cup of shredded carrots and cook for 1 more minute.
Transfer the mixture to a large casserole dish.
Heat 1 tablespoon of vegan butter or oil in the wok and sprinkle in 1 1/2 tablespoons of flour and stir well with a whisk to make a roux.
Slowly add 1 cup of plain plant-based milk to the roux a few tablespoons at a time stirring well between each to get out all of the lumps. (This will become very thick at first, just keep stirring and adding small amounts of more milk and it will thin out.)
Add 1 1/2 cups of vegan sour cream to the thickened milk along with 1/2 teaspoon of salt and 1/2 teaspoon of pepper. (You can also add some red pepper flakes or a dash of cayenne for a little spice.)
Add 1 cup of vegan cheese to the cream mixture and stir well.
Pour the cream mixture over the cooked vegetables and stir it around until it is mixed well with the squash.
Sprinkle the top of the casserole with a generous layer of stuffing mix, breadcrumbs, or crumbled crackers.
Drizzle 3 tablespoons of melted vegan butter over the top.
Bake at 375 F for 30 minutes until the casserole is bubbly and the top is golden brown.
Notes
Allow the onions to cook until they become translucent. Cooking them slowly will make them sweeter.
Slice the squash very thin. This helps it cook thoroughly and gives the casserole a nice texture.
Be sure to saute the veggies before adding them to the casserole. Yellow squash can be very firm and will not soften up enough if you don't saute it first.
If you use zucchini, it will cook a little faster than the yellow squash.