I'm not entirely sure what problem your facing, but if I understood you correctly, while sculpting you can't seek to avoid to fuck up the eyes.
Simple solution for that is just to seperate the eyes before you start sculpting (In edit mode select a part of both eyes, use the + key to select more of the eyes till you get everything selected, ctrl+p to seperate them), and then combining them after your done sculpting (select the eyes, shift click the rest, ctrl + J to combine them)