I'm not sure what you mean exactly, but whatever it is you're wanting to do, you should be able to accomplish it by manipulating the Transform.position and Transform.localPosition fields for the parent and child objects (either in the inspector or via scripting) as needed.

Have a look at the following script :

var parentGameObject: Transform;
var scale = 0.1; // scale of the cube
var gap = 0.01; // gap between the cubes

function Start()
{
    for(var i = 0; i<6; i++)
    {
        for(var j=0;j<6;j++)
        {
            var cube : GameObject = GameObject.CreatePrimitive(PrimitiveType.Cube);
            cube.transform.localScale= Vector3.one*scale;
            cube.transform.position = Vector3(-2.5*scale + (scale+gap)*j, 0, 2.5*scale+ (scale+gap)*i);
            cube.transform.parent = parentGameObject;
        }
    }
}