Why are cooling pipes at the top of the fridge?how is the air left in fridge cooled?

Very basic physics at play... when a liquid is turned onto a vapor via a pressure drop it absorbs ambient heat... when its compressed back into a liquid it expels that heat...

What refrigerant used maximizes the ability with the amount of heat it can move... and safety and practicality. There are many different ways to do this... and not suitable for every given situation.

As far as what tubes are where it depends on the refrigerator.

Well, to be most efficient, the tubes are placed at the highest place in the refrigerator because the warmer air in the refrigerator will tend to rise whilst the cooler air will tend to do down, due to differences in densities. This way, the refrigerator is more efficient