I mark them in the hinge layout inside the mortise, remove the door, turn the gun upside down so I can look at what I'm doing, then lightly punch the holes. This little punch strikes a 1/16 pointed hole about 3/16 deep. I tap it first, take it out and look at it, then if it went where I wanted punchit on in. Put the hinge part inside and screw in the first screw, check the opposite end and make sure the door is exactly where you want it, then lightly punch the hole and check again. If it makes me happy, I punch the hole with the part still in. I tried taking it out, but this way works best for me. Don't do the center hole(s) until you know the door is right. If you mess up then you can file the holes slightly and reposition it, then punch and screw in the last screw(s). Always do the outer screws first.
Susie