I would assume they do it all by trial and error checking connections and wires with nod light or voltometer. The service manual has pretty detailed instructions on how to check most if not all of hte factory wiring harnesses, ECU, MFI, etc.
Also just to correct Blink, it isn't your active aero, it's your ECS computer (no big deal, but whatever)
Seen here:
http://www.3sxperformance.com/faq/ecsmodule/index.asp
Chances are, if all fuses are good, and the wiring on the top of the struts are good. You may have shorted out this computer and need to replace it.