However I was confused about the QNH value which usually a big number on a high elevation airport. And as far as I understand the higher the value the higher the pressure.
The altimeter is measuring the thickness of the layer between two pressures - one you have selected on the sub scale, the other the actual atmospheric pressure sensed by the altimeter.
For the altimeter to indicate altitude above mean sea level the sub scale needs to be set to pressure at sea level.