I think putting the plugs in after paint is the correct way , then the bodyplug hole edge will be sealed with primer and paint ... But....
If you lizard skin the holes you may have heck of a time getting them in (even with the soap trick,thanks! alan)
I would prime paint, plug and , then lizard skin ..or.... I might try masking the plug holes with round patches of masking tape then put the plugs in after or mask the top of the plugs after you install them (put tabs on the tape so once the lizard skin is done ,pull the tape , if you wait youll have a bi...h of a time .. The idea of the plug is to seal and if the dont mate to the lizard skin or go in crooked they wont seal .
Sorry for the long winded idea.