Stir together 2 cups gingerbread mix and 3/4 cup water until smooth; set mixture aside.
Stir together remaining gingerbread mix and brown sugar; cut in 1/4 cup butter until mixture is crumbly. Stir in pecans; set aside.
Combine apple pie filling and remaining 1/4 cup butter in a large saucepan, and cook, stirring often, 5 minutes over medium heat or until thoroughly heated.
Spoon hot apple mixture evenly into a lightly greased 11x7-inch baking dish. Spoon gingerbread mixture evenly over hot apple mixture; sprinkle with pecan mixture.
