How can I make a transparent sclera for the eyes of my model?
It will need to be a different SubTool. You can then assign separate transparency to each SubTool.
Note that this only works if you are doing a BPR render.
See page 117 of the ZBrush4.0_whats_new.pdf and page 53 of the 4R2b PDF. These PDF’s are in your ZBrush installation’s Documentation folder.