Have you adjusted/configured the fan profile in the bios? There should be various settings, ie, standard, silent, performance, in the bios, for controlling fan speeds. Are you running the fans off an integrated hub, or connected directly to the motherboard? I'd recommend running the case fans and cpu cooler directly off the motherboard chassis and cpu fan headers which allows for a greater amount of flexibility when configuring fan speeds. If your motherboard does not have enough fan headers to run all your case fans, you can split each header into two circuits, which is perfectly fine and what I generally do on any motherboard that has only a few fan headers, using these:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812162026