After reviewing your file, I can see you could benefit from the use of Instance names and consolidating your code into one "actions" layer.
Also, if you are just wanting a box to appear in the "over" state of a mouse interaction, you could use a simple button as opposed to a MovieClip symbol.
That being said, it is relatively easy to make the box appear on the top layer.
Just modify the code in the first frame of your symbols to this:
Code:
stop();
addEventListener(MouseEvent.ROLL_OVER, onMouseoverbtn1);
function onMouseoverbtn1(event:MouseEvent) :void {
Object(parent).addChild(event.target);
//this tells the parent object (main timeline) to move MovieClip to the top of its display list
gotoAndPlay("2");
}