I am using a CM Storm enforcer case and i have 3 fans on it, the stock 200mm front fan the stock 120mm rear fan and a Silverstone Air Penetrator AP121-WL 120mm fan as well, and i am not sure where i should position them on my case. I also have 2 lower voltage fan cables (7V & 5V) if need them as well
Put the spare fan as an intake, side of front wherever you can fit it. If you put it in the top as an exaust you'll end having negative airflow which will suck dust into your case. You want positive. The low voltage fans will only help with noise at the cose of performence, if you dont like the noise put them on the two 120mm's not the 200 which should be pretty quiet anyway.