1. Beat first 2 ingredients and 1/2 cup Asiago cheese at medium speed with an electric mixer until creamy. Gradually add flour, beating at low speed until blended. Shape mixture into 24 balls; place on a baking sheet. Cover and chill 1 hour.
2. Meanwhile, melt 2 Tbsp. butter in a medium skillet over medium heat; add onion, and sauté 5 minutes. Add apple and next 4 ingredients, and cook, stirring occasionally, 10 minutes or until golden brown. Remove from heat, and cool completely.
3. Preheat oven to 350°. Place dough balls into cups of a lightly greased 24-cup miniature muffin pan; press dough into muffin cups, forming a shell. Sprinkle bacon into shells; top with apple mixture, mounding mixture slightly. Sprinkle with remaining 1/2 cup Asiago cheese.
4. Bake at 350° for 20 to 25 minutes or until golden brown. Remove from pan to a wire rack, and sprinkle with thyme.