AAAhhhg...so much to deal with. Overwhelming and ANNOYING when I can't get it to work.
I appreciate the help; I'm still trying...
Been there done that.
All computer operating systems are frustrating to one degree or another.
Now that you understand the difference between CPU frequency control and fan speed control, you have half the problem solved.
The basic process looks like this:
1. Enable Cool-n-Quiet in the BIOS. This is necessary to control CPU frequency and voltages.
2. Enable Q-Fan in the BIOS. This option reduces PWM (pulse width modulated) fan speeds with every reboot. The BIOS reduction is only a one-step drop in speed (from full speed to about 55% full speed). To further reduce fan speeds based upon temperature sensors is a function of the operating system but requires Q-Fan to be enabled. Enabling this in the BIOS will reduce fan noise to a less nuisance level, but most people want more noise reduction.
3. Enable CPU frequency regulation. This helps keep CPU temperatures lower.
4. Create a sensors.conf file for your CPU and motherboard temperature sensors. This is the hardest part.
5. Implement a way to start lm_sensors with every reboot. I do this in my rc.local script.
6. Create a fan control configuration file using the pwmconfig command (actually a script). This config file will be used by the fancontrol command (actually a script) to control fan speeds based upon sensor temperatures.
7. Implement a way to run the fancontrol script with every reboot. I created an rc.d script, but my script likely needs some tweaks by other users. You also can start fancontrol in rc.local.
Understand that you can control fan speeds through software only for PWM fans. Not all of the fan connectors on a motherboard support PWM. Also PSU fans are independent of the motherboard. Generic PSU fans are notoriously noisy.
PSUs designed for "silent computing" are much better.
If you have a fan on a separate video card then that fan is not controlled by this method either. Controlling those fans usually requires using the proprietary video drivers and software.
Your Asus motherboard BIOS should have a section where you can view temperature sensors and fan speeds. Record those numbers to provide yourself a guide to whether you have lm_sensors and fan speeds configured correctly.
The good news is after you are done you should have a very quiet or virtually silent box. I'm running a 2.3 GHz BE-2400 dual core CPU on an Asus M2NPV-VM motherboard. Typically the CPU idles at 1 GHz. I have a PSU fan, CPU fan, and case fan. The latter two are PWM fans and controllable. I use the on-board video and have no video card fans. The case is about 6 feet from me and I cannot hear anything from the case. I have to stand directly over the case to hear the fans.