Several of those fan headers are extra special-purpose ones you will not need. The 5-pin EXT_FAN one is a special ASUS design, and it is NOT for a fan, exactly. It is where you can plug in an ASUS custom optional (extra cost) expansion card specifically used to create several more standard CHA_FAN headers for more fans. Few people need these, and you don't, so ignore it.
All fan headers use some temperature sensor to guide them, and the header's automatic control system manipulates the speed of its fan according to the temperature measured there. All mobos have at least two sensors. One always in built into the CPU chip by its maker, and that is always used for the CPU_FAN and CPU_OPT headers, and MAY be available for use by others. Then the mobo maker also has built in a general sensor on the motherboard, located near a component they consider is vital to monitor and cool, and that normally is used by the CHA_FAN headers. Your mobo has more than that. It has a couple extra ones (not clearly shown or named in the manual) on the mobo, plus others.
Some ASUS graphics cards are equipped with a non-standard feature to feed their own internal temp sensor readings back out to the mobo on one card pin, and the mobo has the ability to use those sensor readings to guide selected CHA_FAN headers. So, IF you choose to, you can select a particular case fan that is aimed at the graphics card locations and have its speed guided by that card's cooling needs, rather than by the general mobo cooling needs. I believe the Asus GeForce RTX 2080 Ti 11 GB ROG Strix Gaming card you have includes this feature so you MAY choose to do that. But of course, this means that ONE of your CHA_FAN headers will be configured that way (with its fan suitably positioned), so that header would NOT be used for other general case ventilation control.
So let's go through the main headers. The CPU_FAN and CPU_OPT headers generally behave exactly the same, and both are guided by the internal CPU chip temp sensor. Your idea is right. For the two-fan Noctua air cooler on the CPU, the Splitter included is intended when you have only one CPU_FAN header to use. But since you have both, you can plug those fans separately into those headers. The only real advantage to that is that then the speed signals of BOTH can be shown and monitored for possible failure. Just be sure in BIOS Setup that those two headers are configured identically so they do the same thing. By the way, some Noctua products are shipped with a little device called a Low-Noise Adapter. It is just a small resistor that can be inserted into the cable connecting the fan to its power source. All it does is reduce the fan's voltage supply, and thus its speed, air flow output and noise. It is useful only when you are forced to connect the fan to a fixed 12 VDC supply directly from the PSU and thus have no other way to control the fan speed. When you use the fan with an automatic speed control system on the mobo headers, do NOT install that LNA module in the wiring.
The COV_FAN header is an unusual one, apparently intended to blow cooling air over a cover somewhere. I suspect that one is intended for the metallic cover over the area at top rear of the mobo where the external connection panel is. IF your case has a place in that area to mount a fan aimed there, you could use that, but it's not commonly done. NOTE that this particular header is a 3-pin one, so if you decide to buy and install a fan for this, you can use a 3-pin model, although a 4-pin one would work. But I suspect this header is fixed to use a temp sensor in that area, so it is not suited for use for general case fans.
The AIO_PUMP and W_PUMP headers are intended for powering the pump units of liquid-cooled systems. The AIO_PUMP one particularly is aimed a the All-In-One complete systems, whereas the W_PUMP one is for the pump component of a DIY self-designed system. You have neither, I believe, although your system list does include a hint that you are considering a BeQuiet Dark Rock Pro AIO system instead of the Noctua air cooler. You MAY be able to re-purpose one or both of these headers for general case fans, but I'm not sure (see below).
The three CHA_FANn headers are the ones intended for general case ventilation fans. Your Corsair 780T case includes three 140 mm fans (2 front, 1 rear) of the AF140L type. Corsair does not provide the max current consumption spec for these, but I am sure they are less than 0.3 A each. Since a mobo standard fan header can supply up to 1.0 A max to its total load, you CAN connect all three of these (perhaps even 4 of them, if their max currents are more like 0.2 A each) to a single CHA_FAN header. Although they may come pre-connected to the case's fan speed control system in the top, that system allows NO automatic control of their speeds by the mobo; it is strictly a manual system for which YOU are the controller who decides when and how to set their speeds. You are better to disconnect those three from the case system and connect them instead to a mobo fan header. In doing that you need to make two adjustments because these are THREE-pin fans that must have a header that uses the older DC Mode of control. That is not the same as the newer PWM Mode, so it would be ideal to create two fan groups based on control Mode. Use a simple SPLITTER for these three on one CHA_FAN header configured to use DC Mode, and then connect other 4-pin case fans to a different CHA_FAN header configured to use PWM Mode. Here's an example of a simple Splitter with four output arms. You could use a second one of this same device to connect a group of 4-pin fans to the other CHA_FAN header.
https://www.amazon.com/Computer-Spl...+fan+splitter&qid=1568910278&s=gateway&sr=8-4
Lastly the mobo has a special-purpose M.2_FAN header. Now, you are getting one Samsung NVMe SSD module, and your mobo has two possible places to mount it. See manual p. 1-2 items 6, p. 1-24, and p. 2-11. I suspect the SSD you have can be mounted in either place. The difference I see is that the M.2_1 socket near the bottom places the SSD under a heatsink (must be removed and re-installed) to help cool the SSD. (Note if you do this, there appears to be a tape to remove so that some pre-installed thermal paste on the heatsink can contact the SSD.) IF you choose this location, that seems to be the one for which there is a special temp sensor to guide the M.2_FAN header so any fan connected there and directed at that heatsink location can be guided by the SSD's temperature, and not the main mobo temp.
On many mobos, for several of the fan headers (especially the CHA_FAN and sometimes the AIO_PUMP or W_PUMP ones), there are options that are NOT shown in the manual. So for these you'd have to search inside BIOS Setup to see whether they are available. For the pump headers, you may find you can specify whether they are to be used for a pump of for a plain fan. The plain fan option then re-purposes that header for use with a case vent fan IF you also can choose the correct temp sensor. .For many of these you are offered the option to select exactly which temperature sensor is used by this header for control guidance. If you have that option, select the general mobo sensor for any general case ventilation fans. IF you have fans you plan to dedicate to particular components (e.g. the rear panel of connector sockets and its associated mobo circuits, the graphics card, the M.2 SSD unit). set the relevant header this way. Since the mobo has several special-purpose temp sensors, I am surprised the manual makes no mention of these.