The sensor should be taped to what you want the fan speed to respond to. The problem with this is practicality.... pit it on a CPU and you can't mount heat sink properly
Fan controllers are poor substitutes for what you already have.
1. Mostly they require manual adjustment which makes the name rather inappropriate ... the controller isn't really controlling anything, you are.
2. Thermal sensors have their place when cooling specific items,\you can place the sensors on the surface. So while good for HDs, heat sinks and such, they fail when we think about anything we are actually concerned about, that being CPUS, GPUs and the chips under those heat sinks.
3. Your motherboard already has built in heat sensors.... and your motherboard usually comes with 2 ways to control them. BIOS offers limited control, and the oft included fan control utility offers far more control than a "fan controller"
4. If water cooling, and looking to cool the coolant in your loop, you wouldn't use a sensor taped on the radiator. It will not indicate actual water temp but radiator surface temp and even this reading will be in error as the fans blowing air will cool one side of that sensor. In this case you would use something like this
http://www.frozencpu.com/products/10373/ex-tub-620/Bitspower_G_14_Temperature_Sensor_Stop_Fitting_-_Matte_Black_BP-MBWP-CT.html?tl=g30c229s579
But you can't use these on a CLC type cooler as it has no means to attach it.
5. For fan control I recommend Fan Control PCBs, th best of which is made by Phanteks
http://www.newegg.com/Product/Product.aspx?Item=N82E16811984004
You attach a cable from a PWM (11 fans with power connector) or DCV (typically 6 fans @ 140mm 0.14 amps ... no power cable req'd) header on your MoBo to the input of the PCB (Hub) ... you can then connect the number of fans needed and have the BIOS / utility control all of them