16 ounces 60% chocolate chips or your favorite chocolate bar, roughly chopped, plus 3 tablespoons as needed
In a small mixing bowl, whisk together flours, baking soda, baking powder and salt until evenly combined. Set aside.
In the bowl of an electric stand mixer fitted with the paddle attachment, on low speed cream the butter and sugars until the granules are fully incorporated into the butter, about 3 to 5 minutes. Scrape down the sides and bottom of the bowl, and paddle attachment. Mix again. Add the vanilla extract and mix until combined. Add the eggs and mix for 1 to 2 minutes. Turn off the mixer and add the flour mixture. Mix on low until almost combined. Add the chocolate and stir on low speed for 2 to 3 revolutions until evenly distributed. Stir the sides and bottom with the spatula to ensure there are no patches of unincorporated butter and sugar.
Using a 2-ounce (#40) ice cream scoop, scoop out balls of dough. Flatten into discs, plug any dough patches with chocolate as desired. Place in an airtight container. Refrigerate for 24 hours.
Place an oven rack in the middle position. Preheat the oven to 350 degrees.
Line a rimmed baking sheet with a silicone baking mat, parchment paper or lightly grease with butter.
Arrange the cookies leaving 2 inches of space in between. (Return any unbaked dough, covered, to the refrigerator until ready to bake.)
Bake cookies for 15 to 17 minutes until golden brown but not crispy.
Remove the cookies from the oven. Allow to set on the baking sheet for 2 to 5 minutes before removing onto a cooling rack. Bake the remaining cookies in batches.