The details depend on what mobo you have (and hence, the capabilities of its SYS_FAN headers). Just as importantly, on those details for whatever NEW mobo you plan, IF you are changing. One definite point: you do NOT need a third-part fan controller. The headers on your mobo certainly can do automatic control of fan speeds based on a temperature sensor on the mobo, whereas there are virtually NO third-party fan controllers that can do that. So a fan HUB is the right way, but see below for some notes.
First, as background, automatic control of case ventilation fans (same basics for the CPU cooling system, too) actually is a TEMPERATURE control system. That is, the focus of the control loop is to keep the TEMPERATURE on a specified target, and the method of achieving this is to manipulate the speed of the case fans to do whatever air flow it takes to meet that goal. For this purpose the mobo has a temperature sensor built in at a spot the mobo makers deem is the most important to monitor. The control loop has some pre-programmed items called loop tuning parameters that include the target (as decided by the mobo maker) for that sensor, loop gain and damping, and high temp limit for warnings of real trouble. For each SYS_FAN or CHA_FAN header on the mobo the configuration can be adjusted separately, and options normally include the automatic control system (usually called "Standard" or "Normal"), a fixed constant full fan speed setting, a fixed reduced fan speed setting, and a "Manual" option under which you can specify your own fan "curve" of what speed to run fans for particular measured temperatures. Another common configuration option for any 4-pin header is the control Mode, which is the type of signals the header sends out to its fan. This may be: the older Voltage Control Mode (aka DC Mode) in which the voltage supplpied on Pin #2 varies from 12 VDC (full speed) to 5 VDC (minimum without stalling the fan) and there is no signal on Pin #4; PWM Mode, in which the voltage on Pin #2 is always 12 VDC, and the PWM signal sent out on Pin #4 is used by a special chip inside the new-type 4-pin fan to modify current flow from that power supply through the motor windings; or Auto, in which the header should automatically sense the type of fan connected to it and set its Mode by itself. (Note that, since the older Voltage Control Mode CAN control a 4-pin fan, although not quite as well from a technical perspective, the "Auto" Mode can be "faked" by making the fan header always use only the Voltage Control Mode.) The ONLY Mode that can control an older 3-pin fan is Voltage Control Mode; such a fan given the PWM Mode signals will always run full speed.
Some SYS_FAN or CHA_FAN headers also allow you to choose alternative temperature sensors to guide them in case you wish to customize what one header is used for. The alternative choices may include the internal CPU temperaure (suitable IF this header is controlling a fan actually involved in CPU cooling, such as radiator fans in some systems), or several extra sensors associated with particular key components of the mobo such as the North Bridge chip or the Voltage Reagulator section. These are usful IF you are arranging one fan to cool that specific area of the mobo, as opposed to general case ventialtion.
Note that there are almost NO mobos that attempt to control cooling of an added Graphics Card, mainly because there is no "standard" way to send a temperature signal from that card to the mobo, and no "standard" set of cooling control loop tuning parameters. Graphic card cooling control is left to the card itself. Similarly, no mobo controls cooling of the PSU unit; that is done by the PSU itsef.
Three small additional notes FYI: the header counts the fan's speed signal (a series of 5 VDC pulses, 2 per revolution) sent back to it on Pin #3, but it cannot deal with more than one such signal. So any proper Splitter or Hub will send back only ONE of its fan's speeds and ignore the others so that you will never "see" those others. This has NO impact on speed control because the header really does not care what the speed is - it is focussed on temperature. However, the header has a second separate function: monitoring the speed signal for fan FAILURE (either no speed signal, or a signal below a set minimum value). Upon failure it will send out a warning so you know to take care of the problem. So, when using a Splitter or Hub, you must ensure that one of the fans IS plugged into the only output that can send its fan's speed signal back to the header. Moreover, since the speed signals of all the "other" fans are NOT sent back, those fans cannot be monitored by the mobo header for failure, so YOU need to check them from time to time to verify they are still working.
The CPU_FAN header (and sometimes related ones like CPU_OPT) do the same thing basically, but its temperature sensor always is only the one built into the CPU chip and fed out on one of its pins to the mobo. Further, its actions in the event of fan FAILURE on some mobos are more drastic. If the CPU fan fails, it will issue an immediate warning and may, after a short time, shut down the system completely to prevent overheating even without waiting for the chip's internal sensor to show a high temperature. On such mobos, some also will refuse to start up at all if the CPU_FAN header gets no good speed signal right away. So you must always ensure that the correct item is plugged into the CPU_FAN header so it gets a valid speed signal. For fans on a CPU air cooler that means one of the fans. For an AIO liquod cooling sytem, I believe the right item to plug into the CPU_FAN header often is the PUMP, because its failure will cause overheating very quickly. But if you have a CPU_OPT or PUMP header that does the same failure montoring job, you can use that for the pump and use the CPU_FAN header for the radiator fans.
Splitters and Hubs get very confusing on many websites, in my opinion, becasue the two terms often are misused. I prefer to classify them accordong to eletrical function, rather than by appearance. A SPLITTER is a simple device that connects two or more fans in parallel to the signals from the mobo header, so that all fans share the same information and ALL of the power for the fans comes from the header's Pin #2. There is a limit (normally) of max 1.0 A total current to all fans on this header, so the max current draw spec for every fan connected must be found to ensure the header does not get overloaded. A SPLITTER has only two types of "arms": one input cable ending in a female (with holes) connector that plugs into the mobo header, and two or more male (with pins) outputs for the fans. Among these, one common way to limit the speed signal sent back to the mobo header is to omit Pin #3 on all outputs except one. A SPLITTER may appear to be a group of cable "arms" or a small printed circuit board with male headers; this latter form needs to be mounted securely so that it does not ground out to sopmething by moving randomly. Becasue of the similarity of physical and electrical details of the 3- and 4-pin fan systems, a 4-pin Spltter can work for both types of fans - a 3-pin fan plugged into one of the Splitter's outputs simply will not connect to Pin #4.
A HUB is a different type of device. It does connect the mobo's signals to all its fans in parallel EXCEPT for the power supply line. What makes a Hub different is that it gets power for all its fans from a direct connection to a PSU output (either SATA or 4-pin Molex) and takes no power from the mobo header. Thus it avoids the power limit of the header. That provides to all outputs the fixed +12 VDC on Pin #2 required by a PWM Mode fan signal set. Then the Hub shares the header's PWM signal on Pin #4 to all fans and this does not overload the header. BUT this means that control of the fans' speeds relies entirely on their ability to use the PWM signal to control their own speeds. That is, the Hub works ONLY if connected to a mobo header that really does use PWM Mode and suppply that signal, AND ONLY with 4-pin fans that have the chip to use that signal. (There are a very few Hubs that do thigs differently and "convert" from a 4-pin PWM system input to 3-pin Voltage Control system output that can control both 3-pin and 4-pin fans.) A HUB has the two types of "arms" a Splitter does, PLUS a third "arm" that must plug into a PSU power output, so that's how to distinguish between them.
With that explanation, how to choose? IF you have any 3-pin fans, their speed can ONLY be controlled using the older Voltage Control Mode (aka DC Mode), so they MUST be connected to a header using that Mode. The best way to do this is to use a Splitter and abide by the 1.0 A max current limit. (The unusual "converting" type of Hub is another option.) IF all your fans are of the 4-pin PWM type AND you are confident the mobo fan header actually is using PWM Mode (remeber the "fake" auto Mode configuration?), then use a Hub (often able to handle many fans) that avoids the header's current limit. And that's another reason why you do NOT need a third-party fan contrller, OP. Most (not all) such controllers use only the older Voltage Control Mode which can control the speed of both fan types, but does NOT supply the PWM singal, and therefore cannot be used with a Hub.
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