First, you should understand that a fan with lights in its frame really is two independent devices in one unit. It has a FAN MOTOR which needs power from a mobo fan header like CHA_FAN1, and that header also controls the fan speed. Then it also has LIGHTS (in your case, ARGB type) in the frame that get their power (and control of the display) from a different mobo header. You already have much of this figured out - you do have the fans all working, and the lights work, too. But some details are missing so far. The important thing, though, is that the MOTOR and the LIGHTS operate separately. So we'll deal with the two issues separately.
The Wraith cooler system is a little different because its lights are NOT connected to a mobo header when you are using ARGB lighting. You connect ONLY the small 3-pin cable to a mobo USB2 header and download the proper software. From your post you have done all that correctly, and it works.
The FAN part of the Wraith system is done with its separate attached 4-pin female fan cable that you plug into the mobo CPU_FAN1 header. To get controls of that working, see your mobo manual on p. 80. At the bottom, set the two items shown for that header to Standard Mode and Monitor CPU. Then use the scroll controls to scroll down further to expose the next two lines of options (if they are there). Set the CPU/FAN1 Switch to Fan, and the CPU/Fan1 Control Mode to PWM. This will allow the mobo to use its pre-programmed settings to control the Wraith cooler fan speed according to the temperature measured inside the CPU chip, which will change with your workload. You are not using the CPU/FAN2 header, I believe.
For the case fans you have four. For their MOTORS you write as if there is only one connection to the CHA_FAN2/WP mobo header. I must presume, then, that you are using a fan Splitter or a fan Hub to connect all of the motors to a single header. Now, any mobo fan header can only deal with the speed signal sent back to it from ONE fan. So any Splitter or Hub will send back to its host header the speed from only ONE of its connected fans and ignore all the others. If you look closely at the outputs of the Splitter or Hub, one will be a little different from the others. It may be that one has all four pins, and the other ports have one pin missing. Or there may be some special marking to indicate the special port, or it may be labelled for the CPU fan. Do NOT connect your CPU fan (the Wraith unit) to this. But DO connect one of your case fans to that port, so its speed can be sent back to the CHA_FAN2 header. Then you can "see" that speed, but not the speeds of the other case fans, which will be all the same, anyway. Back on p. 81 of your mobo manual, select the CHA_FAN/WP2 header and set its options as follows: Switch to Fan, Setting to Standard, Mode to PWM, and Temp Source to the motherboard sensor, not the CPU sensor. ALL of this part assumes that the Splitter or Hub INPUT cable is what you have plugged into the mobo CPU_FAN/WP2 header. Right?
When you have all your BIOOs configuration settings made, use Esc to get back to the Main Menu, then F10 to get to the Exit Menu. There choose the first option, Save Changes and Exit, to save your settings and reboot.
NOTE that, from the case web page I could not tell whether the four fans it includes use for their MOTOR cable a 3-pin or 4-pin female connector. My notes above assume 4-pin. BUT of the fan motors have 3-hole connectors, then you will need slightly different settings to be able to control their speeds. And in that case I also would like to know some detail of how the four fans are connected to one header.
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