This was such an ominous title to read in the chit-chat section!
But it looks like you have eyes now, so I assume you figured it out. :D
there are two possible solutions. To make default eyes that "come with" the base HA, you need to drag your eyes layer above whatever's blocking them. Usually this is your Base.
If you want any of the special wearables that are eyes, then put them on like they are clothings and Save. Again make sure they are high enough in the item stack that you can see them and drag them upwards until you can.