Dan, you can control many things like reverb, boost, and FX loops and other functions via the GCX. The loops of a GCX can be used for audio, but are also isolated from each other so they can be used as switches.
In this example, you can see the Mesa head has 4 different functions. Here's how it looks when using a GCX to change them:http://voodoolab.com/gcxdiagrams/05-Ped ... tching.pdf
Also, we'll be coming out with a product called the Control Switcher so you can do JUST this type of stuff without sacrificing the audio loops of your GCX. http://voodoolab.com/controlswitcher.htm
The custom cables come into play when you have an amp that has say a 5-din connector instead of separate jacks. Control Switcher has a multi-pin out just for this type of application. The specific wiring for the cable is different for specific amps.
Hope this clears it up a bit!