I have done it couple ways.
Lately i have been using powder paint tapped through a small hole in an alum. plate then re-heat the head. End result looks decent but has been a steep learning curve to get it consistent after curing. If you cure at too high a temp OR use too much powder on the entire head.......... the eye tends to slide/drip out of the socket. :dodgy: It works best using minimal paint on the head and just using a single color eye.
A different way i tried a while ago, i had painted the pupil with fingernail polish and then went back and placed a bubble of 2-part epoxy in the socket and let dry. It turned out looking really cool, very much like a clear eye with the pupil floating inside. Did have trouble with some of them getting a foggy look though after use and storage.
Wonder if you could paint a pupil then put a drop of the UV Cure Goo - or whatever its called - over top to seal it? No experience with the Goo stuff.... just thinking out loud.