Speedfan is a very odd, very good and very frustrating piece of software in my experience.
For some reason it controls my fans regardless of what the BIOS is set to, but it also won't control a 4 pin PWM fan connected to the CPU FAN header, it will control a 3 pin fan from the CPU header and the same 4 pin fan fine when it's connected to a SYS FAN header, so yeah, go figure.
But I do love it, one of the first things I put on after a fresh build/install. It can be very frustrating to try and figure out all the settings and how they effect the fans, it's also not very intuitive to use and set up, pity there isn't something that does the same job but has a much better GUI to navigate through.