Hi Julie,
What a neat project!
Heres a couple of my thoughts on what youre trying to do:
Ive never had much luck using photopaper for printing images. I cant ever seal them well — the colors run for me at least — so I always use a bright white paper and print on a laser jet.
You could maybe try gluing them on with a clear drying, white glue. I havent tried that on resin, but when I did on acrylic sheet, I always managed to have bubbles or streaks. If I were to do it again, I would try our a light coat of our resin gloss sealer spray or some other kind of spray adhesive.
While the e6000 would give you a good bond, I would worry it would make a goopy mess too. I only use e6000 to glue on bails.
If you do this, would you mind sharing a picture? I would love to see your finished eyes!