The differences among those fan headers is in the particular heat SOURCE they are aiming to cool.
There are two main types of FANS in computers. The older type with 3 pins on the connector are known as Voltage-Controlled fans because control of their speed is done by altering the voltage supplied on the +VDC line (Pin #2). It can range from +12 VDC for max speed down to about +5 VDC for min speed. Lower voltage may cause the motor to stall and not re-start until it is fed a higher voltage. The newer design with 4 pins on the connector is called a PWM fan. In that system, Pin #2 feeds +12 VDC to the motor at all times, and Pin #4 feeds the new PWM signal. Inside this fan type's casing there is a small chip that uses that PWM signal to modify the flow of current through the motor windings, thus achieving speed control. There are a few other connection systems used for powering fans without any control by the mobo.
We all talk about fan speed control, but the truth is that all those fans are parts of TEMPERATURE control systems or "loops" in control parlance. In each case there is a source of heat to be removed, a sensor for temperature of that source (or its nearby space), a control algorithm in the mobo BIOS feeding signals out on the fan header, and a fan (or other device) to cool the heat source. The algorithm is pre-programmed with a target temperature for the sensor and a few loop tuning parameters to scale what signals to send out depending on the actual temperature measured by the sensor, and on known (to the designers) response time chanrateristics of the system. MANY header algorithms also allow you a few other choices, like fixing the fan speed with no reference to real temperature, or setting your own "fan curve" of fan speed versus temperature. In operation the system constantly monitors the TEMPERATURE at the sensor for that header control loop, compares that to its target, and uses that deviation to calculate the correct speed control signal (either voltage or PWM signal) to send out to the fan. The focus is on TEMPERATURE; the fan's speed is only the variable that the system manipulates to achieve that goal.
Fans generate their own speed signal and send that back to the mobo header on Pin #3. But the control algorithm does NOT use that information to control the fan's speed. Another system, though, DOES use that speed signal to monitor it for FAILURE and can take various actions if the speed falls to zero or, in some cases, falls below a set minimum.
A mobo normally has two types of fan headers, but there are sub-types. It always has at least one CPU_FAN header to control the fan (or whatever) cooling the CPU chip. Almost always it uses ONLY the temperature sensor built into the CPU chip itself by its maker and sent out to the mobo on one chip pin. This header's speed monitoring system also is more complex that those for case ventilation because the CPU is so expensive and vital. On many mobos if this fan signal indicates failure, the system will send out an immediate signal (often beeps, maybe a screen message) for a short time, and may even shut the system down without ever waiting for the actual measured temperature to exceed a high limit. Some such systems actually will refuse to start up if the CPU_FAN header does not get an immediate indication of fan start-up. As I said, though, these failure monitoring systems are independent of speed control.
Many mobos also have a CPU_OPT header which operates exactly as the main CPU_FAN header, and it is just to connect a second fan driven by the same signals and temperature sensor, so that you can have more than one fan dedicated to cooling the CPU chip. This is useful, for example, if your CPU cooling device has two fans in a push/pull configuration.
Many people choose to use liquid-cooling systems on today's high-power CPU's, rather than simple fan(s). These consist of a heatsink in contact with the CPU lid that contains a chamber filled with a liquid and circulated constantly by a pump. The pump may be in the heatsink assembly, or a separate component. The fluid is pumped out to a radiator, flows thought that, and returns to the pump. The radiator is mounted near an air grille, and has one or more fans mounted on it to force cool air through it to cool the circulating liquid. Systems like this can be constructed from individual components, or can be bought as a complete system usually called an All-In-One (AIO) liquid cooler system. Control of these systems often is different. Most commonly, the PUMP portion is fed a constant +12 VDC so the pump runs full speed all the time, and the fan(s) on the radiator are the control device whose speed is manipulated by the control system. In a few such systems, the pump speed also may be varied, but that is not common. Control of the rad fan speeds MAY be done by the normal CPU_FAN header, or it may be done by a different control algorithm supplied by the maker as a software utility that must be loaded and run as a background activity under the OS, and communicating with the cooling system from the mobo (often by a connection to the pump unit from a USB2 header). Such a system may need both a fan control header and a pump power supply. For that purpose, the AIO_PUMP header of a mobo is used to power the pump, and usually it does not actually exercise any control over the pump speed. But it CAN provide constant full power, and it can monitor the pump's speed for failure, while control, power and failure monitoring of the radiator fan(s) is done separately.
A mobo also has at least one SYS_FAN or CHA_FAN header to power and control the fan(s) cooling the case and all the rest of the mobo components. Normally this header uses a different temperature sensor built into the mobo at a location its designers consider important to cool properly. Some mobos today allow you to change that and specify use of the sensor inside the CPU chip (not advised, I think) or another sensor built into a particular component of the mobo, such as the voltage regulators or the North Bridge chip. Some users who set up several fans using several mobo headers will set fans to blow on particular mobo areas and use the mobo sensors on those areas to guide those fans. One example of that would be a header pre-programmed to use a temperature sensor in or near an m.2 type of SSD unit mounted in a connector on the mobo - you could position a fan in your case to blow on that device, and use such a header to plug in that fan.
Graphics cards usually contain their own fans and control those fans all by themselves - they do not allow the mobo to do that job. The software utilities that come with such cards sometimes provide you with tools to customize the cooling controls of the graphics card and to "see" that fan's speed, but they still do their own fan control. However, the source of cool air for such a fan is the space near that card inside your case. Your ASUS Strix card has two FanControl II connectors on it to allow you to mount fan(s) in your case that aim their main air flow into the area of the video card, and then plug those fans into these connectors. Then they are NOT controlled by the mobo temperature sensors, they become controlled by the video card according to temperatures on that card.
You have not asked about this last one, likely because you don't have it, but I will describe the PWR_FAN header. It was common perhaps 10 years ago or more. It looks exactly like a normal 3-pin fan header. It is intended for use with a PSU that has a set of three wires coming out just like those of a 3-pin fan, and they are to be plugged into this header. Their only function was to allow the speed of the fan inside the PSU to be communicated to the mobo for display and for failure monitoring. This mobo header does NO control of anything. Control of the speed of the fan inside the PSU, if there is any, is done internally by the PSU itself. Now, since many PSU's did not have this feature, some mobo makers connected the Ground and Power leads also to the pins of the PWR_FAN header, but with NO control capability. Thus, its Pin #2 always has the full +12 VDC supply. That way it CAN be a source of full DC power for a fan or pump, but it is better NOT to use it if you don't have those special leads from the PSU.
Some general guidelines, then.
The main CPU chip cooling system REALLY should be connected to the CPU_FAN header so that it IS controlled according to the temperature of that vital chip. If you have more than one such cooling fan, the CPU_OPT header is useful. If you have an AIO liquid cooler system, follow its maker's instructions carefully. The AIO_PUMP header is useful for the pump portion of many such systems. Don't forget that the FAILURE monitoring functions of these fan headers also are important, and they can only do that properly if you plug the fans (or pump) into their correct headers.
Case ventilation fans are best connected to a SYS_FAN or CHA_FAN header configured to use the general mobo temperature sensor. If you have fans aimed at particular mobo components that have separate temperature sensors provided on the mobo by its maker, you can use those sensors for those particular headers.
Fan headers on a graphics card will be guided by that card's needs, and not by any mobo temperature sensors or cooling needs.
OP, you have a "problem" with six fans and two CHA_FAN headers. I am assuming that this count does NOT include whatever you are using to cool your CPU. There are good ways to handle this situation, including if possible ensuring that all the case ventilation work is done under control by the CHA_FAN headers. (That is, unless you want to devote one of them to supplying air to the Strix card.) Doing this does require, however, that you match the type of fan you have (3-pin or 4-pin) with the abilities your CHA_FAN headers have to use the different fan types. We also have to consider the current consumed by each fan and the max current that can be supplied to fans from a single mobo fan header. So, for detailed help on that, tell us:
What mobo - maker and exact model number.
What fans - count, maker and exact model number of each fan. IF some fans were supplied as part of your case and their identity is not known, tell us the case maker and model, and how many wires come from the fan motor, how many holes are there in the connector on the end of those wires?
With those items we can look up details and determine the best way to connect your fans for full control by the mobo.
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