how to scale an object that uses a mirror modifier? Hope you can help

I have applied a mirror modifier to the below. However - how I can make it so that it mirrors the same result, but on the y and z axis?



Also I am having problems when scaling to make the object more narrow. The first image below is what I want:



However instead of scaling, it seems to just move the object around as though they are two seperate objects (see below). The only way I created the desired effect above was through using clipping, although the tutorial I am following does not use clipping and I don't want to run into any more serious issues down the line... 



Any help much appreciated!
When are you scaling the object you have selected all vertex, all faces so it's scaling through the all plane which is not yet connected to the mirror object. It's ok to use clip checkbox and deselect it after apply every change you want to. To the first question - you've also checkbox "Y" below "X" in the modifier.