Examine the placement of each staple and determine whether the staple is only slightly or overtly jutting out from the carpet.
Yank out all overtly jutting out staples with a pair of pliers. Pull the fibers of the carpet apart with one hand in the area where you want to insert the staple, so you see the foundation or "scalp" of the carpet. Tap in any slightly protruding staples with a nai set.
Press the tip of the staple gun against the bald area and lean all your weight into the staple gun as you squeeze the trigger. Arrange the carpet fibers around this staple. If done correctly, the staple will be in so deep that the fibers will naturally cover it.
Place the tip of a nail set onto the top of any staples that are just slightly visible from the carpet. Jam it downward, exerting, exact, strong pressure. Arrange the fibers around the now flattened and flush staple.