Adjust an oven rack to the middle of the oven and preheat the oven to 400F [200C]. Line three sheet pans with parchment paper.
Form the dough into balls, about 1 tablespoon each [25 g]. Press one ball of the Chocolate Chip Dough and one ball of the Double Chocolate Dough together, but keep their unique colors. Press the piece into a cookie scoop or roll it into a ball. Place 8 cookies on each sheet pan. Sprinkle each cookie with a little flaky salt, if desired.
Bake one pan at a time, rotating halfway through baking. Bake until the cookie tops are golden brown and the cookies are slightly puffed in the middle, about 10 minutes. Remove the baking sheet from the oven and use the back of a spoon to gently press the middle of each cookie to flatten it.
Let the cookies rest on the sheet pan for 5 minutes, then transfer them to a wire rack to finish cooling. Cookies are best eaten slightly warm, but can be stored in an airtight container for up to 3 days.
Cookies will soften the longer they sit. Cookie dough can be formed and refrigerated overnight, then baked the next day; the cookies may need an extra minute to bake if chilled. Cookie dough can also be formed into balls and frozen for up to two weeks: let the cookies sit out at room temperature until the oven preheats. The cookies will need an extra minute if baked frozen.