Fan Speed Control Options?

Noise footprint is kind of a big deal for me. I just built up a new computer and would like to poll the collective here to see if there is prevailing wisdom as to the best way to control both the CPU fan speed and case fans...I have two of the latter. I will shortly replace the AMD Phenom II heat sink with a 120mm fan stood up. The stock CPU fan that came with the Phenom II is whiney.
With my Fractal Design R3 case came a fan controller that can be mounted on the back in a PCI backing plate. So I have the option of controlling my case fans with this knob. Currently I have adjusted all fans in the BIOS...mostly to tune sound with an eye on CPU temp. I am not a gaming guy so cooling of the Phenom II processor even with the modest stock heat sink isn't a big deal.

My question is...what would you guys suggest? Best to circumvent the BIOS control of the chassis fans and use a speed control knob for the case fans? Cooler Master Hyper 212 Plus heat sink I have on order from Newegg is 4 pin which I presume is PWM and therefore RPM can be modulated based from CPU temp. I do have a setting in my ASRock UEFI BIOS that will kick up the speed of the CPU fan if/when the CPU core temp hits 50 deg C. question related to the CPU fan and case there a Windows based software out there where I can control my fans from my desktop without having to go into the BIOS...or using a knob to manually control CPU and case fan speed?

I would appreciate advice on strategies you guys use to control the fans on your there maybe a prevailing recommendation that many believe to be the best approach.

Many thanks.
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  1. Guess you guys don't use fans in your
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