Place squash and onion in a large microwave-safe bowl. Add a few tablespoons of water. Cover with platic wrap and microwave for 3 to 5 minutes. You want the squash to be crisp-tender.Drain well and blot dry with paper towels. Place in a 6-quart slow cooker.
Scatter the butter and Velveeta on top. Cover and cook on LOW for 1 1/2 hours.If not tender enough, cook longer.
Stir and check for seasoning. Add salt and pepper to taste.
If you want this dish spicy, add 1/2 teaspoon of crushed red pepper flakes.