In addition to this when I attached the Heatsink/Cooler Fan to the Motherboard over the CPU is the fan is facing towards the outside of the case. It is pointed directly at a fan which came attached to the case. Should the fan be facing towards the outside of the case or toward the inside of the case.
It is generally the case that air is taken in through the front of the case and drawn out the back. So your heatsink should be facing towards the rear of the case so that air in drawn throught the heatsink fan and out the back of the case.