Depends what part and where it is. Best to install pins before paint so any marks can be repaired if necessary. I will usually install the pin in the mirror or door handle first then just eyeball where the corresponding hole needs to be in the body. For more accurate placements or multiple pins, I have used short sharpened pins in the part (not glued in) to mark where the corresponding holes need to be. For something like a bumper, I might drill the hole in the body rom the outside, tape the bumper in place and then from the inside, drill out into the bumper…carefully so as not to go right through.?
I added some rubber tips to a set of tweezers to hold small parts. A pin vise is better for controlled drilling of shallow holes than a spring loaded push drill.