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Beat together the butter, salt, sugars, extracts, egg, and yolk until light and creamy.
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Add the flours and mix until well combined.
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Divide the dough in half, shape each half into a rectangle, wrap in plastic, and chill for 1 hour or longer.
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While the dough is chilling, make the chocolate topping: Heat 2 cups of the bittersweet chocolate in the top of a double boiler (or in a microwave in 30-second increments) until very soft; when you stir it, it should be almost fully melted.
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Add an additional 1 cup of the chocolate, stirring until smooth and fully melted; this is a basic way of tempering the chocolate, which will keep it shiny as it sets. See "tips," below.
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Place the chocolate molds from your butter cookie set on a baking sheet, and spoon the melted chocolate into the molds. You'll need about a heaping teaspoon of chocolate per mold.
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Once all the molds are filled, gently tap the pan to help remove any bubbles in the chocolate. Allow the chocolate to set until hard; refrigerating the molds will help speed up this process.
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Once the chocolate is hard, gently remove each piece from its mold then refill the molds with chocolate (re-tempering it if necessary).
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Repeat the process five more times, using up the remaining chocolate, until you have 48 chocolate pieces.
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To bake the cookies: Preheat the oven to 350°F. Lightly grease (or line with parchment) two baking sheets.
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Place one piece of dough on a lightly floured work surface, and roll it 1/8" thick.
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Cut out rectangles of dough using the cookie stamp from a butter cookie set; it helps to dust the stamp with extra flour. Place the cookies on the prepared baking sheets.
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Bake the cookies for 10 to 12 minutes, until they're just starting to turn golden.
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Remove the cookies from the oven, and allow them to cool completely.
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To assemble the cookies: Gently spread a thin layer of melted chocolate on the back of each chocolate piece (to act as glue), then place one on top of each cookie.
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Allow the chocolate pieces to harden in place before serving or gifting.
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Store cookies, covered, at room temperature for up to several days.