Use Shift + left-mouse to label atom. Do the same to toggle off the label. The font size is changeable using Edit -> Font Size.... The newly centred atom is labelled by default. To turn this off use:
(set-label-on-recentre-flag 0)
Some people prefer to have atom labels that are shorter, without the slashes and residue name:
(set-brief-atom-labels 1)
To change the atom label colour, use:
(set-font-colour 0.9 0.9 0.9)