Preheat your oven to 375 degrees.  Spray a casserole dish with cooking spray.  Add the cubed squash. Set aside.

In a medium skillet, over medium-high heat, melt 1 tablespoon of butter.  Once the butter is melted, add the minced onions, sage, and thyme. Cook, stirring often until the onions are translucent and just beginning to brown, approximately 6 to 9 minutes.  

Carefully remove all of the thyme stems.  If the leaves have not fallen off while cooking, you can pick them off and add back to the pan.  You do want to remove the stems.

Pour the onion mixture over the squash and toss to mix completely.

Cover the dish with foil and place in the preheated oven.  Bake for 50 minutes or until the squash is almost tender.

Meanwhile, pour the crackers into a ziplock bag.  Using a flat meat mallet or bottom of a wine bottle, crush the entire sleeve of crackers to fine crumbs.  Mix the parmesan cheese and the remaining 4 tablespoons of butter into the cracker crumbs.

Sprinkle the crushed cracker mixture on top of the squash.  Return to the oven and continue to cook for an additional 15 minutes or until the crackers are browned.

Remove the casserole from the oven and allow to cool for 5 minutes.  Serve warm.