The key part in speedfan is setting your motherboard PWM fans to "Software controlled" (now called Manual I noticed) in Options for your chipset, then try to increase or decrease various speeds until you find one that affects your fan (you'll probably find one for your CPU too). Don't forget to untick "Automatic" on the main screen other the arrows do nothing!
Do not assume that numbers match and that Speed03 is your fan, maybe it's your cpu fan showing? Set them all to manual and try them one by one. On my board, the cpu fan is shown as case fan, somewhow.
Do not assume that your motherboard supports fan control on all your fans. Some board circuitry only support control for the cpu fan, some on cpu + one other fan only. Rarely are all fans controllable. Check your manual (or google) for PWM support. Try other fan ports. Try disabling any fan option in BIOS (use the "always on", "max", "not intelligent" or similar option)
Do not worry about speeds. Put your case on the table and look inside while doing this. Some fans do not report speed properly, but can still be controlled. Speedfan sets speed according to temperature, so you don't even really need to read the RPM. You just have to find the % at which your fan stops working by looking at it.
Check that your fan supports PWM, too. Some don't. Most do.
That said, Speedfan rocks.