I believe the chipset fan should be connected as shown here:
http://www.tomshardware.com/motherboard/20050103/images/asus-a8n-sli-big.jpg
Does your chassis fan have 3 wires? It won't read the speed unless it has 3 wires. SpeedFan will regulate the speed nicely even if it cannot read the speed.
Disable QFan so it doesn't conflict with SpeedFan. Load SpeedFan and set it up to control the CPU fan using Temp1. There are several items to set in SpeedFan to enable fan control, so use the following to verify your setup. My recollection of how to set up SpeedFan follows (I may miss something since it has been a couple of months, so double check check using SpeedFan's HELP).
Configure Temperature Page: first line, click on name, set Desired temp to 30C or whatever is reasonable for your system. Set Warning temp to 48C or as needed. Click the + at the start of the first line and check the box on the line whose sensor is Pwm1 .
Similarly for the second line except click on the box whose sensor is Pwm2. You can change the name of the temperature using F2 if desired, e.g. I changed the second temp to NF4. The "Sample" column should show the temperature read from the associated sensor.
Configure Fans Page: boxes for first 2 items checked
Configure Speeds Page: First two lines checked. For each of these, click on the name, set Minimum value=50%, Maximum value=100%, check Automatically variated.
Configure Advanced Page: select 8712F, set PWM 1 mode to "Software Controlled" . Same for PWM 2 mode.
On the main SpeedFan screen, check "Automatic Fan Control"
I have SpeedFan load automatically at startup. It takes a minute or so to ramp the fan speed down to inaudible at startup.