The ports on a mobo marked SYS_FANx are intended for use with case fans. Within the BIOS Setup screens you will find that one or both of them offer to provide control of the fans' speeds, too. (Automatic control is enabled by default usually, but you can change.) The automatic control loops use a temperature sensor in the mobo and vary the voltage to the fans to alter the fans' speeds and achieve stable temperature at the setpoint. The alternatives offered usually include setting those fans' speeds to fixed values, or setting them to full speed at all times.
Many mobos today have 3- or 4-pin fan connectors, and fans come with either 3- or 4-pin connectors. They are designed so that both 3- and 4-pin fans can connect to any 4-pin mobo pinout and work properly. BUT a 4-pin fan MUST connect to a 4-pin output on a mobo.
3-pin fans work by varying the voltage supplied to the fan (red + VDC, black ground), and the yellow lead simply feeds a pulse speed signal generated by the fan back to the mobo for monitoring and displaying. 4-pin fans use a different speed control system called Pulse Width Modulation, and a different set of line color codes. The fourth line contains a "square wave" type of signal, except that its "% on" time is varied. Within the fan itself, that signal is used to control how much of the +12 VDC supply is fed to the motor for speed control. If you plug a 3-pin fan into a 4-pin output port, it will work because the PWM signal simply is not used by the fan. However, you may have to tell the BIOS Setup screen that you are using a 3-pin fan there so that it knows how to set up the +VDC line to achieve fan speed control.
There are two mobo fan ports that you generally should NOT use for case fans. FOR SURE you do not connect a case fan to the CPU_FAN port - that is for the CPU fan only. You may have a port labeled PWR_FAN, and it is intended for connecting a special lead set form the PSU so that the BIOS gets a speed signal from the internal PSU fan and can check it. But some have found that this port can power a normal case fan, probably with no ability to change its speed.