Saute onion and jalapenos until limp, about 3 min. Add garlic and saute 2 min more.
Whisk in flour, making a roux, stirring constantly over low heat 2 to 3 min until flour is very pale gold. Whisk in milk, stir constantly until thick and bubbly, about 3 min. remove from heat and stir in cheese
Pour sauce over squash in casserole. Top with the 1/2 cup shredded cheese
Bake uncovered 28-30 minutes until cheese is melted and browned on top.