I cant seem to be able to find a way of controlling my CPU fan speeds either through the BIOS or through software like Speedfan. I can however easily control the speeds of fans in PWM headers.
Would there be any problems in doing this?
More aboutissue putting 4pin header
Nope. Not an issue at all. However, connecting a 3-pin fan to a 4-pin PWM connector will not allow for PWM to work. It will just be a regular fan that you should be able to adjust to some degree in your BIOS.