3pin fans are analog, DC voltage controlled. There's 3 wires, a hot, ground and tach. The hot wire can be from 5v to 12v or 7v to 12v, depending on the fan. This equates to 40% or 60% to 100% duty cycle in bios. Basically a 1000rpm fan at idle speeds will spin at 400rpm or 600rpm depending on if it's a 5v low or 7v low. And then raise to 1000rpm at 100% (12v)
4pin (aftermarket style) are PWM. They have 4 wires. 12v hot, ground, pwm signal and tach. A PWM fan always is fed 12v, constant. The bios sends a signal by the signal wire that looks like Morse Code. This has the affect of turning the fan off/on. The longer the pause between bleeps, the slower the fan spins. A PWM fan at any value less than 100% is always in a state of trying to start. Because of this and a 12v constant, PWM fans go as low as 20% duty cycle, so a 1000rpm fan at idle speeds is only at @ 200rpm ±.
There's 1 fundamental difference between the cpu_fan header and sys_fan headers. The cpu_fan header is dedicated pwm. It will not control a 3pin DC fan. It's a constant 12vDC. The sys_fan headers are interchangeable, depending on how you set them in bios. If set for DC, the 4pin PWM fans will struggle, if set for PWM then a 3pin fan won't change speeds.
To use 2 fans on any header you'll need a splitter. A 2way pwm splitter has 2x sets of wires joined to 1 connector. 1 set has 4 wires, standard hot/ground/pwm/tach. The other set only has 3 wires, hot/ground/pwm. You only want 1 fan to report its speed to the motherboard, the pwm signal is sent to both, based on the 1 fan speed.