Updating prefab information live

How can you update a prefabs position values live if it is already in game view?

For example, if i have a prefab of a cube and its XYZ position values are all set at 1. And if i place that prefab into the scene view, but its position values are being set all at 5 and its following way points. If i spawn an object into the game(via mouse click) and i want it to follow that cube, it will always go to the prefab coor'ds, meaning 1. How can i change that value so the cude will actually move towards it?

EDIT:

Here is what i am doing at the moment:

var target : Transform;
var smooth = 5.0;

function Update()
{
    transform.position = Vector3.Lerp(transform.position, target.position, Time.deltaTime * smooth);    

}

Explanation: When my Player gameObject hits an enemy collider (which is bigger than the enemy gameObject) this script will be activated so a prefab(which is just a square at the moment) will 'fire' at the enemy target to destroy it.

It appears your spawned object are referencing the prefab itself and not the cube in game. On your object spawn you should have it just pull a reference to the thing you want it to follow in game. That will ensure it follows the correct object.

Assuming you're doing something like the samples here: http://unity3d.com/support/documentation/ScriptReference/Object.Instantiate.html

You would have something like (from that page)

var clone : Rigidbody;

clone = Instantiate(projectile, transform.position, transform.rotation);
clone.transform.position = whereever you want it

and use 'clone' in your Update script to set its transform.position to follow the cube