.. Put the coupling nut into the chuck and tighten it
evenly, taking the slack out of all three jaws. (Just put the chuck
key in each hole in turn, taking out any slack. If you tighten a
Jacob's chuck at only one point there will always be some slack in
the other two positions, usually enough so that whatever is chucked
will not run true.)

The hole you choose to tighten a chuck has no bearing on the centering of
the jaws. They're all on the same screw.