Heat oven to 375°F. Spray 13x9-inch (3-quart) glass baking dish with cooking spray.
In 10-inch skillet, cook beef, salt and pepper over medium-high heat 5 to 7 minutes, stirring frequently, until beef is thoroughly cooked; drain.
Meanwhile, in 3-quart saucepan, melt butter over medium-low heat. Add onion; cook about 2 minutes, stirring occasionally, until tender. Stir in flour. Cook 1 to 2 minutes, stirring constantly, until bubbly; remove from heat. Stir in thyme.
Stir milk into onion mixture. Heat to boiling, stirring constantly. Boil and stir 1 minute; remove from heat. Stir in 2 cups of the cheese until melted.
Spread half of the potatoes in baking dish. Top with beef; spread remaining potatoes over beef. Pour cheese sauce over potatoes.
Cover with foil; bake 45 minutes. Sprinkle remaining 1 cup cheese over potatoes. Bake uncovered 15 to 20 minutes longer or until top is brown and bubbly and potatoes are tender. Let stand 5 minutes before serving.