In terms of loads on the PSU output bus(ses), there is no difference whether the fans are connected to the PSU or to a mobo header. The power still comes from the PSU's 12 VDC bus. However, it does make a difference to control - the mobo automatic systems cannot control any fan plugged into a PSU output connector.
There is a way that you can connect four of your fans to your two mobo SYS_FAN headers. First, some "rules" that impact this scheme:
1. The SYS_FAN headers on your mobo (see manual, p. 30) may have 4 pins, but they are NOT "4-pin headers" that use PWM Mode for control. They are clearly marked to use Voltage Control Mode (as all 3-pin fans require).
2. You have two 4-pin PWM type fans. Although they are best used on a PWM Mode header, they DO work under mobo speed control when connected to a 3-pin header operating in Voltage Control Mode. So those fans can connect to your mobo.
3. The "stock fan that came with the case 4 pin" I also assume is a standard 4-pin fan intended for PWM control. That is, the "4-pin" label you put there means its connector is just like the connectors on your Noctua and Corsair fans, and not a 4-pin Molex male connector. Right? Assuming that, it also can be used on your mobo headers.
4. As a "rule of thumb" you can connect up to 2 normal fans to any mobo header - I have seen posts saying more is also acceptable, but two certainly is. So if you buy two 4-pin fan Y-splitters like this,
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423160&cm_re=4-pin_fan_splitter-_-12-423-160-_-Product
you can connect up to four fans (either 3-pin or 4-pin type) to your two SYS_FAN headers. Note that these splitters send to the mobo port the speed signal of only ONE of the two fans connected to it, and the other is ignored. This is the correct way to design a splitter.
So, those two splitters and your three 4-pin fans can get you 3/4 of the way to connecting to your two SYS_FAN mobo headers. The last part is how to plug in one of your older fans that has only a 4-pin male Molex connector on its wires. There is no simple adapter for this, so you'll need to do a little bit of custom wiring. There are two key things to know to make this easy. One is that the connection to the mobo only needs to have two wires, not three or four. And the other is, the wire color codes will match up so make things simple.
First, you also buy one 3-pin fan power extension cord like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812189006&cm_re=3-pin_fan_extension-_-12-189-006-_-Product
On this you cut off the male connector (the one with pins) on one end, leaving you the female 3-pin connector on the other end. Now just roll up the YELLOW wire and tape it - you will not use it. Now, go to your fan that has two wires (Red and Black) coming out to two different Molex connectors. Cut off those two wires near the connectors - you don't need the large Molex connectors. Now, strip wire ends and connect Red from the fan to Red on the extension cord, and Black to Black. Twist them or solder them (better), and wrap the joints in tape to insulate. Now you have a fan with a 3-pin female connector on the end, and you can plug it into one of the Y-splitters you have. If you look at those splitters carefully, you will see that, of its two output male connectors, one is missing Pin #3 (the speed signal line). So plug your modified old fan into this splitter output, since the old fan does not have a speed signal (yellow wire) from it anyway. The fact that you have connected a 4-pin fan and a 2-pin fan to one splitter to share one SYS_FAN header is not a problem at all. Both of them will be controlled by the variable voltage supplied by the mobo header on the Red and Black wires.
Do it this way - two 4-pin fans via a 4-pin splitter to one SYS_FAN header, and another 4-pin fan plus a 2-pin fan (with modified connector) on a different 4-pin splitter to the other SYS_FAN header - and you can connect all four fans to those headers. Then the mobo's automatic control system that operates those headers can control all four of your fans for you to cool the case. The actual CPU cooler, of course, is completely separate, and connected to the mobo CPU_FAN header.
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