The word from Alphacool is that it does not detect component temperatures via the USB cable, but through sensors attached to the controller only.
The easiest way to do this is using a sabertooth mobo. The sensors are already on the board and the ai program it comes with lets you set custom fan profiles via a graph. Ie you can ramp the speed up slowly as the temp increases. Or have no fans on till you hitt 100 c, if you're that insane.
That's what we've been discussing in the thread There isn't a mATX version of the Sabertooth board, sadly.
Hmm... SpeedFan should actually do exactly what you want. You have atleast two fan-headers for case-fans on any modern motherboard, so you can atleast control one fan in the front and one in the back with SpeedFan. Depending on the used fans and their powerdraw, you can even use a simple splitter-cable to connect two fans to each fan-header on your motherboard, letting you control 4 fans with SpeedFan. All without any additional sensors, purely based on the inbuilt sensors for your CPU and GPU-temperatures.