Combine your dry ingredients (both flours, baking soda & salt) in a mixing bowl. Give the ingredients a quick stir to combine. Set aside. Use a sharp kitchen knife to chop 8 ounces (2 bars) of chocolate, set aside as well.
In a separate large mixing bowl combine the butter and both sugars and beat on medium speed using a handheld mixer or a stand mixer for 1 to 2 minutes, until the butter and sugars are combined. Scrape down the sides of the bowl as necessary. Add in the eggs and vanilla extract and continue mixing on medium speed to combine. Stop the mixer and add in the dry ingredients, with the mixer on low speed mix everything together just until the cookie dough forms. Dough will be thick and sticky. Add the chopped chocolate pieces to the bowl and use a large spoon or spatula to fold the chocolate into the dough. Use a cookie scoop to scoop out cookie dough balls and place them on a small baking sheet. Cover the cookie dough balls with plastic wrap and set the baking sheet in the refrigerator to chill for a minimum of 2 hours but preferably over night.
Preheat oven to 350 degrees. Line a baking sheet with parchment paper and chop the remaining chocolate bar for the cookies.
Place cookie dough balls on baking sheet, giving them about 2 inches of room between each cookie. Bake in the oven for 6 minutes. Carefully remove the baking sheet from the oven and lightly press pieces of chopped chocolate onto the cookies (careful not to burn yourself) and return the cookies to the oven for an additional 5 to 6 minutes to finish baking (11 to 12 minutes total baking time). Remove cookies from the oven and allow them to cool for about 10 minutes before transferring them to cool completely. Cookies are best when fresh but stay soft and chewy when stored in an airtight container.