There is a very simple way to do what you say you want, but that depends whether that really IS what you want. IF you really want to have control of the fans yourself, rather than letting your machine do it all for you, that is a different matter.
Your mobo has automatic fan speed control systems already, and you can set it to use those and not have to worry. For that you do NOT need Speedfan at all. You do need to know how to get into your BIOS Setup system, make a few adjustments (maybe) and save them. If you tell us the maker and exact model number of your mobo, we can look up its manual and advise more precisely.
For now, a general explanation. We all talk about automatic fan speed controls by the mobo. But in reality each of them is a TEMPERATURE control system. It monitors an actual temperature from a sensor on the hot item, and then manipulates the speed of a cooling fan aimed at that item to keep its temperature near a good target so it does not overheat. As you change your workload and the heat generated causes temperaures to rise, the fans automatically speed up (or slow down) to keep up with the cooling needs. You do not have to do any work for this. These systems also do added tasks, like making SURE the fan starts up at boot time, and checking to be sure the fan has not stalled, etc., and sending you a warning if a fan fails. Part of this also is never to send the fan a signal to stop and, conversely, to force the fan to re-start if it ever does stall. (A few mobos allow you to let the fan stop at low temperatures and re-start when needed, but that is not common.)
In your mobo there will be at least two separate fan control systems. One uses the CPU_FAN header (and maybe a related one) to control cooling of the CPU. Its basis is a temperature sensor inside the CPU chip. The other (there may be more than one) is for case ventilation fans, and its basis is a different temp sensor built into the mobo. SOME mobos may even have extra temp sensors on special components on the mobo, but you do not usually need them.
Each fan header is configured separately in BIOS Setup, and there are several items for each. You may have an option to disable a header if you have nothing connected to it.
(a) PROFILE is the type of strategy used to determine what speed the fan shuld run. Its options include usually Standard or Automatic (continuously monitors the relevant temperature sensor and uses that to decide the fan speed using a pre-defined "curve" of speed vs temp), Turbo for always full speed, Quiet for always slow speed, and Custom or Manual (similar to Automatic, but allows you to set your own "curve" specs).
(b) MODE is the method it uses to send signals for speed control to the motor. Options are Voltage Control Mode (aka DC Mode) required for 3-pin fans, or PWM Mode ideal for 4-pin fans.
(c) SOURCE may allow you to choose which temperature sensor this header pays attention to.
(d) ALARM may allow you to set a lower limit for fan speed to trigger a failure alarm, or perhaps an upper temperature limit for this sensor to trigger an alarm.