By "pin count" I mean how many wires and pins coming from ONE fan. The reason I ask is that different control methods are required for 3-pin fans and 4-pin fans. So here's what you can do easily.
For the two 4-pin fans attached to your Noctua cooler system, plug one into the CPU_FAN header, and the other into the CPU_OPT header. I think you have done this already. They will be controlled by the same automatic system.
For the two 3-pin fans for case cooling, plug one into each of the CHA_FAN1 and 2 headers. They have 4 pins sticking up, but the fan connector will only cover three pins on each.
Now you need to go into BIOS Setup to configure the fan headers. See your mobo manual on p 2-6 to start. To get into BIOS Setup, turn on the machine and immediately press down the "Del" key and hold it down until the opening setup screen appears. Normally it will show you Easy Mode (p 2-7) and then you press the F7 key to get to Advanced Mode (p 2-8).
On the main menu across near the top click on Monitor. See p. 2-36. Scroll down to CPU Q-Fan Control - see item 2.7.4 on p. 2-37. This should be set to "PWM Mode" for your 4-pin fans, and lower down set the CPU Fan Profile to "Standard". Scroll down further to section 2.7.5 on p. 2-38, Chassis Fan 1/2/3 Q-Fan Control, and set this to "DC Mode" for EACH of your CHA_FAN headers. (You probably have to set each of these headers separately, and not make just one setting for them all.) Next item Chassis Fan 1/2/3 Q-Fan Source should be set to "MotherBoard". Then set Chassis Fan 1/2/3 Profile to "Standard". Now use the F7 key again to return to Easy Mode (p. 2-7) and use the F10 key (prompting note at bottom centre of screen) to SAVE and EXIT. This will same all those settings you just made and re-boot your system.
Those adjustments will set things this way:
Your two CPU cooler fans on the Noctua system will be automatically controlled by the mobo (using PWM Mode for the 4-pin fans) according to the actual temperature measured inside your CPU chip by a sensor, with details of the control strategy pre-set for you. The two case cooling fans will be powered and controlled automatically by the two CHA_FAN headers they are plugged into, using DC Mode (required for your 3-pin fans), based on a different temperature sensor built into your motherboard, and using its own group of pre-set parameters.