In my case I use textures to simulate the pulpills (when it is cartoon character). I just have to keyframe the texture moving on Y axis to make the eyes blink.
As for the rotation problem, I recommend these:
-Animate your rotation in local mode (LCL). This way you can be sure that your object's axes will not change when crossing global axes.
-You can build a direction constraint. This will force the X axis to always face the reference object. So, you can control the rotation of the spheres by moving an invisible object placed just in front of the character's face. The reference object should be child of the head.
-If you want to get more into the above technique, you could even build another bone to control the reference object. The bone's root has to be right in the middle of the eyes, the effector placed right in front of the eyes, and the reference object position-constrained to the bone's effector. The effector can even be the reference object. So moving the effector would move the pulpills.
Hope this helps
Bernard Lebel