Maybe I'm reading it wrong, but I don't see why you don't just build the head as normal with the beads imbedded/ encased in the Sculpey? It bakes at a low enough temperature that most beads shouldn't have any issues.
My eye beads are something like styrene plastic I suspect. I buy them second hand at markets, as strings of white plastic beads. And what I found was, leaving them embedded in unbaked sculpey for a few days, the beads started to dissolve and mix with the sculpey. They also go soft if heated, even the heat from drilling them if you go too fast, but they do survive baking in foam latex at 100 degrees celsius. I don't know if they would survive baking at the temperature required for polymer clays (130 c I think) but a test is worth trying. Glass beads worked ok and could be baked in the sculpey, but I couldn't countersink an iris in them, I had to stick with the basic cartoony white-bead-with-a-black-pupil type of eye. The Delrin balls sold by Marc Spess at www.AnimateClay.com might be better for that. I don't know what Delrin is, need to ask Marc.
With my Sculpey Adam and Eve puppets I baked them with glass balls in open sockets, but no eyelids. Then I removed the glass bead and put in the plastic eye bead. I used latex to form the eyelids over the beads so I wouldn't have to bake again. But the latex had a tendency to peel off the sculpey if I wasn't really careful when loosening them over the bead so it could rotate freely. I did it 3 times before I got it right. Not an ideal solution.