Well, you have to do some bookkeeping with your clones, array is fine for that.
When a box is clicked you should search the array to find top box and swap y position with it.. or whatever you want to do then.
Thanks Finjogi, I have been able to do that. But what I need if for all boxes above the one clicked to slide down one position.
Example:
There is 5 boxes stacked on top of each other.
If I click on box 3, boxes 4 and 5 should slide down 1 position and box 3 should take box 5's position