A 3-pin fan's speed is voltage level controlled. The SYSFAN1/SYSFAN2 connectors on the motherboard use voltage level control for the fan speed. Connect your 3-pin fans to these fan headers if you want to control their speed in MSI Command Center.
The CPUFAN1/CPUFAN2 connectors use PWM (i.e. Pulse Width Modulation) to control fan speed and require a 4-pin fan. If you plug a 3-pin fan into these fan headers they will always run at full speed.