Since your mobo provides 4-pin ports for all its fans, you really should buy 4-pin fan - aka PWM Mode fans - for all positions.
First, make sure to plug the CPU cooling fan into the CPU_FAN header and nowhere else. Do not plug a different fan position into this port. The mobo does a few extra things to monitor the CPU cooling and protect the CPU chip, so this port needs to have the CPU fan on it.
Next, your four case ventilation fans, versus two mobo ports. First of all, get the PWM versions of the Noctua fans - they are the right ones to use with these mobo ports. Next, buy two 4-Pin Y-splitters for your fans. Each of these allow you to connect TWO fans to ONE mobo port. An example:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423160&cm_re=Y_Splitter_4-pin_fan-_-12-423-160-_-Product
It is acceptable to connect two fans to one port, but not more - the limit is in the brief start-up current to get the fans running. I'd suggest putting the two intake fans on one port and splitter, and the two exhaust fans on the other. Let the mobo's fan control systems for each of its three fan ports do their default automatic control.
The PWR_FAN port on your mobo is only for a particular use, and maybe not for you. SOME PSU's come with a set of three wires coming out that end in a "standard 3-pin fan" connector. IF yours has that, plug it into the mobo PWR_FAN port. All it does it allow the fan in the PSU to send its speed signal to the mobo for measurement and info. It does not actually do any control of the PSU's internal fan. If that fan changes its speed, that control is being done entirely within the PSU itself. But if your PSU does not have these special wires, then connect nothing to the PWR_FAN port.