Well then, if you plan on doing an OC, you should definitely get an aftermarket cooler, the Hyper 212+ is a popular choice among the people of this forum. Install the cooler and use AS5; not the generic stuff that comes with the CPU or the Hyper 212+. If the temps go down, the problem was likely due to a bad thermal paste application.
Other areas to look are your fans - make sure they're spinning properly and spinning the correct way (intake vs. exhaust); ensure there isn't any thermal paste on the CPU pins; also check the heatsink fan - ensure it is also spinning properly.
In terms of fan configuration, you'll have to decide for yourself. Just know that there is a difference, but the question that matters to every individual is: "Does it matter?" Personally, I have negative air pressure because I leave both of my side panels off, but left on, my case pressure would be more or less neutral. Simply research positive and negative air pressure here:
http://www.tomshardware.com/forum/238184-31-case-airflow-positive-negative-pressure
Cases can make a big difference in the way the air pressure vents. Make sure that your wiring isn't bunched up anywhere there is air flow (basically tuck your wires/cables in one of the empty HDD bays).