Unless your characters have a very unique style, their eyes will have to look at something. Based on this idea, there is a common practice of making this "something" a bone where the eyes will always point to. This is very useful when animating, since you can position this bone to the exact place where your character should look at without further worries.
003-Eyes.blend. This file has a head mesh with two eyes ready for you to work on them. Notice that the eyes are separate objects from the head.