Yep, it all depends where they are in the display list.
so in this example clip 2 is on top
var container : Sprite = new Sprite();
var clip1 : Sprite = new Sprite();
var clip2 : Sprite = new Sprite();
container.addChild(clip1);
container.addChild(clip2);
and in this example clip 1 is on top
var container : Sprite = new Sprite();
var clip1 : Sprite = new Sprite();
var clip2 : Sprite = new Sprite();
container.addChild(clip2);
container.addChild(clip1);
Just think of it as a big old stack of cards. Take one from the middle and put it on top and that's the one you'll see.