I came here hoping for some advice on how to tame the fan controls on this board. [...] I've set all the fans to the silent profile.
I'm currently using GA-Z97M-D3H (haswell) mobo with UEFI and it's pretty good when it comes to fan control. But I can share a few tricks - if your mobo is similar.
"silent" is not the quietest mode. Even quieter is the "manual" setting + you have to choose 0.75W/'C stepping
CPU fan header has DIFFERENT fan speed profile than SYS1 and SYS2 fan
CPU FAN header starts @60% fan speed and ramps up (silent mode)
SYS1 and SYS2 FAN headers start @30% fan speed and ramps up (silent mode)
but remember that SYS fans ramps up only if MOBO temp goes up
If your CPU fan is too loud - and can be slowed down without overheating CPU- you have 2 choices:
a) just switch to a fan with SLOWER max speed - standard fan is usually rated @1500rpm max, you can switch to a fan that is rated @800rpm max. In this case your fan will be spinning @500rpm when idle and max out @800rpm. With a good cooler and 120mm fan it should be enough to cool CPU when gaming.
b) if you have @1500rpm fan and don't want to buy a new slower one - just connect it to the SYS1 or SYS2 header and see if it's enough to cool your CPU - if it's not enough you can experiment with fan "manual" mode and bump up speed progression (like 1W/'C)
I'm using best of both options (at least for me) - I have 1500rpm CPU fan hooked up to SYS1 header so it starts @500rpm and then - when OS boots up - I can control the fan speed via software relatively to CPU temp. Best thing is that I can override that bios settings and I can speed up SYS1 fan to it's max rated speed (if I need to).
Keep in mind that I'm on macOS system (hackintosh) and using HWmonitor software. But at least I know it CAN be controlled via software, so there is a chance that SpeedFan will be able to control it too.