Preheat oven to 350F. In a medium bowl stir together flour, cocoa powder, and baking soda; set aside
In a large bowl, beat together butter, 1/2 cup granulated sugar, brown sugar, and the 1/4 cup peanut butter until combined. Add egg, milk, and vanilla; beat well. Beat in as much of the flour as you can. Stir in remaining flour mixture. Form the chocolate dough into 32 balls about 1 1/4 inches in diameter. Set aside.
For filling, combine powdered sugar and 1/2 cup peanut butter until smooth. Shape mixture into 32 (3/4 inch) balls.
On a work surface, slightly flatten a chocolate dough ball; top with peanut butter ball. For each cookie shape the chocolate dough over the peanut butter filling. Roll dough into a ball.
Place balls 2 inches apart on an ungreased cookie sheet. Lightly flatten with the bottom of a glass dipped in the 2 tablespoons sugar.
Bake cookies in preheated oven for 8 minutes or until just set and surface slightly cracks. Let stand 1 minute. Transfer to wire racks; cool.
TO STORE: Place cookies in layers separated by wax paper in an airtight container; cover. Store at room temperature for up to 3 days or freeze for up to 3 months.