Let's try to reduce the confusion. First, you should understand that there are two fundamentally different fan groups. The FIRST is the fan(s) used to cool the CPU, whether that's just one, or two. All the fans in this group must be connected to the CPU_FAN or CPU_OPT headers, because those two use as their guide a temperature sensor built into the CPU chip. The second group are those used to cool the case interior, and these should all be connected to mobo CHA_FAN headers, of which you have three.
Next, recognize that, in BIOS Setup (see your manual, p. 2-6 to get there, use the F7 key to get to Advanced Mode (p. 2-8), then use F6 to get to Q-Fan Tuning (p. 2-37)) you need to select each of the FIVE fan headers and configure each in turn separately. When you have them all configured, you use the Esc key to get back to Main Menu, then click on Exit on the top menu bar to get to the Exit Menu (p.2-48). There choose the option to Save Changes and Reset.
You have five fans in total, all of the 3-pin design, according to your posts above. IF you have TWO of those on the CPU and the other 3 on case vent, this is easy. However, if only one is for the CPU and you have FOUR for case vent, then there's a slight change to make.
We'll start assuming you have TWO fans cooling your CPU. Those two should be connected to the CPU_FAN and CPU_OPT headers. In BIOS Setup (p. 2-38) configure EACH this way:
CPU Q-Fan Control to DC Mode (suited to 3-pin fans)
CPU Fan Profile to Standard (normal automatic fan speed control)
Then, for the THREE fans used for case ventilation, see p. 2-39. For EACH, set:
Chassis Fan n QFan Control to Enabled
Chassis Fan n QFan Source to MB to use the motherboard temp sensor for guidance
Chassis Fan n QFan Profile to Standard (normal automatic fan speed control)
Allow Fan Stop to Disabled so the fan never stops completely
Note that for these three headers you do NOT have an option to set DC Mode. The CHA_FAN header design actually only operates in the older DC Mode, so that's fine for your fans.
Now, IF you have only ONE fan on the CPU, and FOUR cooling the case generally, then make one small change. Do NOT connect any fan to the CPU_OPT header. Buy a simple SPLITTER like this
https://www.newegg.com/p/N82E168124..._re=coboc_fan_splitter-_-12-423-160-_-Product
and use it co connect two fans to one of your CHA_FAN headers. The rest is unchanged.
This will ensure that all of your five fans are being controlled properly by DC Mode. The actual CPU cooling fan(s) will be guided by the CPU chips' internal temp sensor, while the case cooling fans will be guided instead by the general-purpose sensor on the mobo. All of them will have their speeds adjusted automatically by the mobo to keep the relevant temperatures under control. FYI, the NORMAL process at start-up is that ALL fans start at max speed to be sure they do start. Then, in a few seconds, the system gets temp readings and slows the fans down to whatever is needed,
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