In a medium saucepan, over medium heat, melt the butter and the 12 ounces of semisweet chocolate chips. Stir constantly until just melted. Remove from heat and let stand for 5 minutes to slightly cool.
In a large bowl, combine the brown sugar, eggs and vanilla. Beat with an electric hand-mixer, on medium speed just until blended. Beat in the cooled chocolate mixture just until combined.
Add the cocoa powder, flour, baking powder and salt. Mix on low speed just until combined. Cover bowl with saran wrap and refrigerate for 2 hours.
Preheat oven to 325 degrees F. Line two cookie sheets with parchment paper. Scoop and drop the cookie dough by the tablespoon, onto the prepared cookie sheets. You should fit 12 cookies per sheet, and making sure to space them at least 2 inches apart.
Bake cookies for 12 minutes. Remove cookies from oven and place one piece of chocolate on the center top of each cookie, and then top each chocolate with one half marshmallow. Place cookies back in oven and bake another 4 minutes.
Remove pan and let cookies cool at least 5 minutes before transferring to a cooling rack.