Begin by preheating your oven to 350 degrees F and lining two sheet trays with parchment paper. Take 6 of your 12 soft caramel square candies and cut them into 4 pieces each using a sharp paring knife—this will give you smaller caramel pieces to place on top of the cookies before baking.
Next, slice your 16 1/2 ounces of refrigerated chocolate chip cookie dough log into 12 equal portions. Take one piece of dough and flatten it into a small disk, then place one whole caramel into the center. Top it with another piece of flattened dough and form the two pieces together into a ball, completely covering the caramel in the middle. Repeat this process with the remaining cookie dough and caramel candies until you have 6 stuffed dough balls.
Evenly space the dough rounds onto your parchment-lined sheet trays, making sure to leave at least 2 inches of space between each cookie to allow for spreading during baking. Top each cookie with 4 of the small caramel pieces you cut earlier, distributing them across the surface of the dough. Bake for approximately 14 minutes, or until the cookies are golden brown and set around the edges.
Remove the cookies from the oven and immediately sprinkle them generously with flaked sea salt while they're still hot—this timing allows the salt to adhere to the warm caramel and cookie surface. Allow the cookies to cool on the sheet pan for about 3 minutes before serving warm, which gives them time to set slightly while still maintaining that gooey caramel center.