In 12-inch skillet, melt 2 tablespoons of the butter over medium heat. Add sweet onions and thyme; cook about 20 minutes, stirring occasionally, until soft and golden. Stir in salt and pepper. Remove onions from skillet; set aside.
Heat oven to 425°F. Spray large cookie sheet with CRISCO® Original No-Stick Cooking Spray. Unroll pizza crust dough on cookie sheet; press dough into 14x10-inch rectangle. Bake 7 to 11 minutes or until light golden brown. Reduce oven temperature to 375°F.
Meanwhile, in same skillet, melt remaining 1 tablespoon butter over medium heat. Add apple and sugar; cook 4 to 6 minutes, stirring occasionally, until sugar is melted and apple is slightly soft.
Spread onion mixture over partially baked crust. Top evenly with chicken, apple mixture, bacon, green onions and cheeses.
Bake 10 to 20 minutes longer or until cheeses are melted and crust is golden brown.