I made up a little guide here for those of you looking to use Speedfan to control the fans in your system.
Note: Speedfan is not guaranteed to work properly with all motherboards so use it at your own risk. Go to http://www.almico.com/forummotherboards.php
to check for compatibility with your board.
First go into your motherboards bios and disable any automatic fan controls This is important to avoid any conflicts which may cause system hang-ups or other undesirable side effects!!
Next download Speedfan
and install it. The program will scan the various sensors on the motherboard and you should see your fan speeds and some temperature readouts in the main window.
Next click on configure button and go to the option tab. Two settings need to be changed here. Ensure the "Set fans to 100% on program exit" button is checked. If it's not checked the fans will stay at the last setting you left them at when exiting Speedfan, even if the temperatures go way up! Also set "Delta value for fan speeds" to it's maximum setting, this way the fans spin up quicker when using automatic fan control.
Now navigate to the advanced tab. Here we find the chip selection tab. Select your boards superIO chip from the list. There should be a list of items that appears. What we are looking for is the PWM mode which needs to be set to manual PWM control. Now the fan speed percentage can be changed using the up/down arrows under the main temp/fan monitoring window. Note that setting the speed lower than around 30% or so can result in strange rpm readings or even cause the fan to stop spinning.
For setting up automatic fan control navigate to the speeds tab...
Click on the fan control you want to set up and set the minimum and maximum speeds you want to it to run at. Check the "Automatically variated" box. You can also uncheck the box next to any unused PWM's to clean up the main monitoring window. Also you can rename any item by clicking on it and pressing the F2 key.
Under the temperatures tab we find the setup window for the various sensors. I'll use mine for an example...
Expand the temp sensor item you want to change and check the corresponding fan speed control on the list. In my case I have the cpu temp activating both the cpu and chipset fan to simplify things a bit. Clicking on "CPU Temp" opens up a selection on the bottom for desired temp and warning temp. I have my desired temp set 3 degrees higher than my normal cpu idle temp. As soon as a load is put on the cpu both the chipset fan and cpu fan spin up to the maximum speed set under the speeds tab, then fall back to minimum speed when the cpu is idle again. Experiment with the desired temp until you find the optimum setting. Warning temp will show a little flame icon next to the sensor readout in the main window, as well as triggering all fans to run at 100%, as soon as the warning temp is reached. Don't forget to check the "automatic speed control" box in Speedfans main window as well.
When finished configuring everything place a shortcut to Speedfan in your startup folder to make it run when the computer is started.
That's pretty much a basic setup, you can also setup the fans to run independent of each other or change the "fan delta value" so they spin up slower if you like.