Preheat oven to 350°F.
In a large bowl, whisk together the flours, baking soda, baking powder, and salt. Set aside.
Using a mixer with a paddle attachment, cream butter and sugars until light and fluffy (3 to 5 minutes).
Reduce speed and add eggs one at a time, then add vanilla.
Slowly add dry ingredients, mixing until just combined. Fold in chocolate chips by hand.
Drop spoonfuls (2-3 tablespoons) of dough onto a baking sheet.
Place caramel in center and form dough around the caramel candy. Place back on the baking sheet.
Sprinkle cookies with salt. Bake for 10-12 minutes.
Let cookies cool a few minutes on the baking sheet before transferring to a wire rack. Serve warm. If the cookies have cooled completely, warm them up in the microwave for 15 seconds to soften the caramel.