Preheat oven to 350 degrees F. Line a 9 inch square pan with foil and spray foil with cooking spray.
Make the filling first. Beat the cream cheese and both sugars together with a mixer, then reduce speed and beat in the pumpkin, egg, vanilla and pumpkin pie spice. Stir in the flour. Set aside.
In a second bowl, beat the butter, salt and sugar until creamy. Beat in the eggs and vanilla. Stir in the melted chocolate chips then stir in the flour. Pour all but about 3/4 cup of the chocolate mixture into the pan.
Spoon the pumpkin mixture evenly over the brownies layer.
Drop reserved brownie batter over pumpkin to give the brownies a splotched, marbled look.
Bake on center rack at 350 for 45-50 minutes or until brownies test done. That is, when a skewer inserted comes out clean. Let cool for about two hours at room temperature and then chill for a few hours or overnight (the longer the chill, the better). Lift from pan and cut into 16 large squares.