In the bios under hardware monitor there is an option for the temps and the fan speed and you can select options in both. you can enable or diable the options. If the bios is controlling the cpu fan then I doubt that you can change it with speed fan and if you diable it then the fan will not work unless you set the speeds in speedfan.
Just out of curiosity why do you need to increase the fan speed? Are you getting high temps with the cpu? Is the bios not increasing the fan speed when needed?
Acording to the description of what speedfan does it is capable of changing the speeds of fans so if in your case you can't do that then maybe it's not clear in the software how to do it or you need to uninstall it and redownload it and install it again.http://www.almico.com/sfdownload.phphttp://download.cnet.com/SpeedFan/3000-2094_4-10067444.html