How many fans connectors do I have

There are two connectors for fans that cool your CPU chip - they are CPU_FAN and CPU_OPT. IF you are using a liquid-cooling system (AIO liquid cooler) for your CPU chip, there is a special header called AIO_PUMP for that type of system. But I am not exactly sure how it needs to be used. If that is your situation, I'd suggest asking ASUS and the cooling system supplier for advice via their respective Tech Support lines.

For case ventilation fans, there are two main headers, plus a third different one. The two common ones are CHA_FAN1 and CHA_FAN2. Each of these can supply up to 1.0 amps total to all fans attached to it. Although a header is built for one fan, you can use splitters to connect more than one to a header, subject to that current limit. The third header, H_AMP_FAN, apparently does the same thing but has a higher limit on total amps. What that limit is, is not specified. The manual says that all of these fan headers (and, indeed, the ones for CPU use) can work with either 3-pin or 4-pin fans; they all are configured by default to detect the fan type connected and adjust the4mselves automatically, but you have the option on each header to set just one of those modes. This gives you lots of flexibility, but I advise one limit. On any one header if you connect more than one fan (e.g. by using a splitter), keep all the fans on one header to the same type - either 3-pin or 4-pin.

The last and not-common header is labeled EXT_FAN. This is a special header to be used only with an optional add-on card you can buy from ASUS. You connect this card to this special header, and then you can plug even more fans into that card. Without that card, this header is not to be used.

Splitters are simple devices that allow you to connect two or more fans together to one header. They can be used in either 3-pin or 4-pin fan systems. They are subject to the limit of the maximum amperage available from a header for all of the fans connected to it, because the header is the only source of power to its fans. When used, a Splitter supplies all its fans with the same power and control signals.

A different device, a 4-pin fan HUB, can be used to connect several fans to a single header. A Hub can only be used with 4-pin fan headers that use PWM Mode for control (all of yours do this) and only with 4-pin fans. Where they differ from Splitters is in power limits. A Hub gets power for all its fans from a connection directly to a PSU power output (either 4-pin Molex or SATA) and thus is not limited by the header's power limit. When used, the Hub sends the same PWM control signal from its header to all its fans.

Both Splitters and Hubs do one important thing. Any mobo fan header receives a speed pulse signal from its fan on Pin #3. It can measure and display that speed. It also can monitor that signal for fan failure. But it does NOT need that information to do its fan control functions. BUT the header can only deal with a speed pulse signal coming from ONE fan. So, all decent Splitters and Hubs will feed back to their mobo headers the signal from only ONE of their fans, and the others are ignored completely. So you will never see the speeds of the other fans on the Splitter or Hub, and the mobo cannot tell you if one of those fails.

Combining your 2 threads into this one, I'll add based on info from your other thread. There you add that you are using a Kraken X52 liquid cooler system for your CPU, and you will use three PWM - type fans for case cooling.

The Kraken manual, as you say, instructs you to connect the pump unit itself to the mobo's CPU_FAN header via a 3-pin connector, then to connect both of its radiator's fans to the special fan leads coming off the pump unit. It also needs a power connection to a PSU SATA power output, and a communication connection to a mobo USB2 header. Lastly, once it's all assembled, you download and install Kraken's CAM software that takes over the control of CPU cooling. With this system you will not need the CPU_OPT or the AIO_PUMP headers, as you anticipate.

With only three 4-pin fans (PWM fans) for case ventilation, your simplest arrangement is to connect each of them individually to the two CHA_FANn headers and the H_AMP_FAN header, and let each of them be powered and controlled individually by those headers. You don't need anything else.

OK, for four PWM fans I suggest you get two of those splitters and use them to connect two fans each to the CHA_FAN1 and CHA_FAN2 headers.

Regarding the "missing pin", see the last paragraph of my first post. The METHOD by which a Splitter like that manages to ignore the speed signal from the second fan is that is second output connector is simply missing the Pin #3, so there is no signal connection for the second fan's speed signal. On each splitter, both fans will be fed the same voltage. If both fans are indentical, they will run at virtually the same speeds.