I would use the probes, or a few of them, but I would not use them to control any fan speeds. I would use the probe temps as a general gauge of the systems health. As an example. I would tape a probe to the top of the base of my cpu heatsink, here's a picture.
With a probe located here it won't tell you your actual cpu temperature, but you can use it as a reference point. You can then run a few load tests and make a rough correlation between the temperature reported by the probe and the temperature reported by a Utility like HWMonitor
Once you position all your probes and finish all your basic temperature tests you can then start testing what the effects are on individual components by adjusting your fan speeds, using your controller.