I've done this just experimentaly, but as a rule I don't do it anymore. I haven't found that eyes make any difference one way or another. That's just my personal opinion.
However, if you are powder painting it's a pain in the back side, but you can do this. Take a paper plate or some small flat surface and pour out a little "pile" of powder paint. Heat your jighead up and then dab it in the pile of paint. Flip it over and do the other side. It takes some practice - and ruined heads - before you get the right size of eye and right shape.
What I have done in the past with powder painted heads already is use a water based paint and an eye dropper to dab the eyes on. After that though, you have to clear coat the head so that the water based paint will not come off. The technique is a lot easier this way. But the pain with this is having to go back and clear coat the heads.
All of this isn't worth it to me. Your mileage may vary. :D