most motherboard BIOS chips have several settable options for fan controls, or OEM applications that will allow the used to configure how many fans are used, and how fast they run according to circumstances.
In the case of BIOS settings, you normally get a choice of DEFAULT - normally controlled by internal temperatures, ON - full blast, or USER DEFINE, where you dial in what speed you want it to be.
Most boards from 07 onwards have PWM controls on all the fan sockets, which means that you can balance the airflow though the PC case AND control the CPU fan speeds in relation to the ambient within the case itself.
This is a big help to those of us who run two GFX cards in SLi (or crossfire) mode, where you have a big hotspot over the PCI-E slots, right under the exhaust from the CPU which in turn cools the heatsink of the chipset.
It's all a big balancing act; on the one hand, you want to keep everything within the case reasonably cool, but by the same token you don't want to be using more power (and making more noise) than really necessary.
I hope this is helpful.