There are a few things you need to understand when it comes to powering and controlling fans. But we'll start with fan design types.
There are three main designs of fan in use now for case ventilation, labeled by the number of wires coming out of the fan (and hence the number of pins or holes in the connector on the end of the wires). There are some with only 2 wires (red and black) that usually end in a larger connector about ¾" wide that has space for 4 round pins in a single line inside a shroud, but there may only be 2 pins there. This type can only be plugged into a female (with holes) power output from the PSU called a "4-pin Molex" or maybe "Peripheral" output. More commonly there are fans with 3 wires (Black, Red, Yellow) ending in a smaller female (with holes) connector that can plug into a mobo fan header. (A fan header on the mobo looks like 3 or 4 pins standing up with a plastic tongue sticking up beside the first 3 pins.) These are called "3-pin fans". The newer design, "4-pin fans" has 4 wires coming from the fan, and ending in a female connector with 4 holes.The connectors and wiring arrangements for 3-pin and 4-pin fans are very similar to create limited compatibility, with the result that you CAN plug either fan type into either of the two male mobo header designs, and they will work - sort of. All 3- and 4-pin fans plugged into a mobo header will receive power and run. However, in the specific case of a 3-pin fan plugged into most 4-pin fan headers, that fan can only operate at full speed all the time. This is because the method of controlling fan speed is different for those two fan designs.
Using an adapter, you can arrange to plug a 3-pin or 4-pin fan directly into a PSU power output, the same as a 2-pin fan would. But ANY fan plugged into a PSU directly will only run full speed all the time - the PSU has no way to control fan speeds.
CONTROL
The speed of a 3-pin fan can only be controlled by what is called "Voltage Control Mode" or sometimes "DC Mode". The wires to a 3-pin fan are Pin #1 (Black) Ground, Pin #2 (Red) +DC Voltage supply, and Pin #3 (Yellow) Speed Pulse signal. To power and control this fan, the mobo header varies the voltage sent out on Pin #2. The Speed Pulse signal on Pin #3 is generated inside the fan motor and sent back to the mobo where it is counted to display the fan speed. This signal actually is NOT used for speed control purposes. However, it is monitored to be sure the fan is running, and failure (no speed signal) will usually trigger an alarm message; in some cases it can even trigger a shut-down to protect against possible overheating.
A 4-speed fan header sends out very similar signals on its first 3 pins, except that the Pin #2 signal is always the full 12 VDC. Then it sends out on the additional Pin #4 the PWM signal. Inside the motor of a 4-pin fan there's a small chip that uses that PWM signal to modify the power coming in on Pin #2, changing how much of that power gets through the motor windings and thus controlling its speed. A 3-pin fan plugged into such a header has no such chip inside and hence no wire to get that PWM signal. So it would only get the fixed +12 VDC signal on Pin #2 at all times and run full speed.
A mis-match the other way - plugging a 4-pin fan into a 3-pin header - will control the speed of the 4-pin fan, although that's not quite ideal and it fails to use some of the advantages of the 4-pin system design.
MOBO HEADERS
All 3-pin headers can operate only in Voltage Control Mode. They can all power and control both 3-pin and 4-pin fans.
There are several variations on how 4-pin mobo headers operate. The intended "standard" way is that they use only "PWM Mode" as described above. Some mobos offer you an alternative in the part of BIOS Setup where the fan headers are configured. They allow you to specify whether the header uses PWM Mode or Voltage Control Mode (aka DC Mode), so you can manually adjust them for the type of fan you are using. Some mobos claim that their headers can detect automatically which type of fan you have plugged in and set themselves to the correct control mode. There are a LOT of mobos now that have 4-pin headers on them BUT actually run them only in Voltage Control Mode (aka DC Mode) and do not use Pin #4 at all. This makes them "universal" for many uses, because that mode is NECESSARY to control any 3-pin fan, and it CAN control any 4-pin fan although it's not quite ideal. The only problem this creates for users is that a header that does NOT use PWM Mode cannot be used with most fan HUBS, because these devices (used to connect many fans to one mobo header) only work with 4-pin fans and PWM Mode control systems.
OP, the particular mobo you have, according to its manual, has one SYS_FAN header that uses only the standard PWM Mode. (We are not talking here about the CPU_FAN header that is used ONLY to control the cooler on your CPU chip.)
SO, OP, back to your problem: your fan(s) are noisy, probably because they are running full speed all the time. Why? And what can be done to change that?
Why? Could be any of three causes:
(a) the fan(s) are of the 2-pin type and are connected to a PSU output, and not to a mobo header. This always means the fans will run full speed. To change that your easiest path is to replace the fan(s) with ones of the 4-pin type which CAN be controlled properly by your mobo's SYS_FAN headers, and then plug them in on the mobo.
(b) Your fan(s) are of the 3- or 4-pin type, but they are connected (using an adapter) to a PSU power output, and not to a mobo header. A related possibility I did not mention above: your fans MIGHT be connected to a "Fan Control" system built into your case which allows you to set their speeds MANUALLY, but does not have them automatically controlled by a mobo header. If they are connected to the PSU but DO have small standard "fan connectors" on the fan wires, you should be able to change that and plug the fan(s) into the mobo SYS_FAN header. If they are plugged into some case-mounted Fan Controller, maybe you can use that to adjust your fan(s).
(c) You have only 3-pin fan types, but they are plugged into the mobo SYS_FAN header. That header cannot control any 3-pin fan's speed, because it can only use the PWM Mode to exercise control. In that case, the best solution is to replace the fan(s) with 4-pin design ones that CAN be controlled by such a header.
One more point. You write as if your case has only one ventilation fan in the back. I assume you do NOT mean the one that is inside the PSU box; you mean a separate fan mounted inside the case rear panel to blow out. BUT are you sure there is only one? IF you have more than one case ventilation fan (an intake in the front, for example), you will need an additional small accessory to get them all plugged into the single SYS_FAN header you have on your mobo.
So, look closely through your fan system. Assess how many fans you have for case ventilation (do not include the CPU cooling fan). For each one, check how many wires come from it, and what they are plugged into. Post back here and we can advise what options you have to improve and make them quieter, but still provide effective cooling for your system.
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