As a general rule, remember that hot air rises. Which means that intake fans should be as low as possible and outtake as high as possible.
If you have a flat top case, you could install an extractor fan there, blowing upwards. Besides, if you have a PSU with a 120mm fan beneath it, it plays a role too, in extracting the hot air.
Basically, there should be an equal input/output. Because of the reasons madgary mentioned.
And, if you don't feel like cutting your case to bits and drilling it like swiss cheese, you could invest in a better ventilated case. Like CoolerMaster's RC-690, for example. It doesn't cost an arm and a leg and has very good airflow. It comes with 3 120mm fans and you can stuff in 4 more. The only inconvenient is it still costs money.