The ASRock mobo BIOS fan settings are not very well written IMO. Compared to what I got on Gigabyte Mobos, it is retarded. On Gigabyte, it gives you preset settings (normal, silent etc.) as well as two threshold temp settings (low and high) so that it can scale the fan speed between the two properly. As we know, mobo and CPUs started at around 20C or so. So a base low temp point of 20c is appropriate to effectively control the fan speed as temp rises. On ASRock, it only has the top temp settings. The low end seems to be fixed at 0C which doesn't make any sense. As a result, in order to achieve lower fan speed, you need to lower the target fan speed setting which I assume will affect the final fan speed when temp rise real high. I just put in a PWM case fan which rotates from 2000 to 6000 rpm. If I only adjust temp settings, the fan will still scream at around 3500 rpm at 20c temp. I have to effective lower the target fan speed to lowest setting for it to settle down to 2000 rpm.
I now have my CPU FAN target at stage 5 instead of 9. And case fan at lowest 2. Both fans run at their lowest speed right now. Need to verify if CPU temp rises, whether or not it can ramp up the speed.
BIOS settings apply when PC boots up. AXTU software settings only apply when that software is loaded (which you can ask it to load at start up). Two basically does the same thing. So, I'd stick with BIOS settings.