The phrase "to cook the waffles" means to prepare and make the waffles by applying heat to the batter until they are fully cooked and ready to eat. Full definition
Cook your waffles according to the waffle iron instructions or make pancakes with the batter as you desire. (userealbutter.com)
Press down on lid to close (use lid lock if you have one) and cook waffle until golden brown, 8 — 12 minutes depending on your iron. (bonappetit.com)
If you are making a large batch, set up a baking sheet with a wire rack inside and place cooked waffles on the rack and keep warm in a low oven. (theheritagecook.com)