I feel like the only real way to make this work is if each set of eyes contains three poses: left eye, right eye, both eyes.
That way, if you have something covering one eye or the other, you can equip the single eye pose. I feel that might solve some of the limitations regarding the eyes layering over things--not all the limitations, but some of the more obvious ones at the very least. I'm going to cookie this, but again, I'd like to see poses to equip just one eye or the other, if possible, that way it opens up the diversity of the animated eyes, just a little. =)