Line 3 large baking sheets with parchment paper or with nonstick baking mats, such as Silpats. Dip a 2-inch round cookie cutter in flour, and mark circles 2 inches apart on prepared sheets. Transfer pate a choux to a pastry bag fitted with a 5/8-inch plain tip (such as an Ateco No. 808), and pipe puffs to fit in flour circles. Smooth peaks with a moistened finger, rounding tops to ensure even rising. Freeze pastry puffs on baking sheets until firm, about 30 minutes.
Meanwhile, sprinkle a clean work surface with 1/2 cup granulated sugar, and place tart dough on top of sugar, patting it into a round. Sprinkle another 1/2 cup sugar over dough, and roll to a scant 1/8-inch thick, coating both sides of dough with the sugar to keep it from sticking. Using a 1 1/2-inch cookie cutter, cut out 36 rounds, and place a round on top of each frozen puff. Return to freezer until firm, at least 15 minutes. Preheat oven to 375 degrees with racks in upper and lower thirds.
Bake puffs until pale golden brown all over, 25 to 30 minutes. Let cool completely on baking sheets on wire racks. Puffs can be stored in an airtight container at room temperature overnight.
Put heavy cream in the bowl of an electric mixer fitted with the whisk attachment. Beat on medium-high speed until stiff peaks form. Whisk the pastry cream to soften. Working in 2 batches, fold whipped cream into pastry cream. Transfer to a pastry bag fitted with a 1/2-inch plain tip (such as an Ateco No. 806). Insert tip into bottom of each puff, and fill. Dust with confectioners' sugar. Cream puffs are best eaten within a few hours; refrigerate in an airtight container.