I have gotten in the habit of adding a sphere to the scene and set it so that its not visible in the raytrace scene.  I then point the eyes to that and parent the sphere to the aux camera (which I use to render, I use the main for posing etc).  That way I can use the sphere to pont the eyes off camera or directly at it and if you move the camera, they will track with it.  If I have multiple characters in the scene, I name and colorize the spheres so its easy to distinguish them when creating the poses.   You can also use a similar technique on the head as well to make the head track with the camera or off to one side of it.  For head tracking I usually use a box instead of the sphere and then point the head at the box, the eyes at a sphere.  The box gets parented to the camera, the sphere to the box.  You can then detach the box from the camera if you want and the eyes will stay relative to the head. 

The heirarchy window stays open for me most of the time :)