So, what do you want to do exactly. If you could provide an example on how you want to control the fans it would be much easier to explain

First thing to do is get Aquauite 2012 running.
It will make everything much easier.
2nd thing is to name all your sensor, fans and devices to something meaningful so its easier to setup a controller.

Then go to controllers in Aquasuite and choose a controller type to add with the plus sign. Currently you cant do curve controllers from here but a set point controller will work well enough to you learn how it all works. Then you can get into doing a custom curve controller from the front panel once youve learnt how it all works.
Ok add a setpoint controller and add a temp sensor or some other useful sensor as a data source that you want to control the fans speed
Then select the output corresponding with the fan you want to control.
Adjust target temp . The Factor P & I defaults are fine if what your measuring temps of only changes slowly. If its a fast changing temp sensor and if you want a faster adaption to temp change adjust Factor P to 400 and Factor I to 500 to start with. Hysteresis is the tolerance for temp change, I have mine set for 0.1 for accurate temp tracking. A setting of 1 will mean the temp can vary up or down by 1c without changing the fan speed.

For alarms you have to use the front panel and its not a simple task i will go into here. You need to also have the 2pin relay connected to power switch in parallel or the ATX cable adapter to turn the PC off incase of flow failure or other events such as over temp.
I advise you to just play with it and try some temp alarms to start with and see how they work before trying to trigger an automated shutdown.