It depends. My bios for example does not have an option for controlling fan speed, only whether or not I want it monitored, and at what rpm do I want to see a warning.
Another option is a program called 'speedfan', but it seems to only work with a limited number of motherboards.
A third option is to purchase a manual fan controller. Something like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16835118217
See what some others say.