I purchased my CM HAF 932 last August. My tower style cpu heat sink has two 120mm fans. I connected those two fans to my motherboard. I connected all other fans to the power supply. I do not use a fan controller. I simply let fans operate at full speed.
Your own set-up will depend on what you want. Do you want to be able to control fan speed? If you do, then you can connect a few fans to the motherboard. Motherboards have anywhere from two to four fan connections. The remaining fans can be connected to a fan controller.
There have been numerous threads at Tom's Hardware concerning fan speed. The main reason for reducing fan speed is to reduce fan noise. However, fan noise is subjective. One person's quiet fans are another person's "jet engine".
the stock fans run at maximum of 700rpm (except for exhaust which I think is at 1400rpm max) so unless you replace them with 120mm which can run faster a fan controller is pointless, the fans are silent anyway, I bought a bay-fan controller in the hopes of getting them faster until I realised they were at max speed anyway, I keep the fan controller in anyway because it's got built in card readers but it does seem a bit of a waste of money.