The lead for the phatnoise head unit came at last. and so the blue plug was fitted into the Skoda stereo, ran under the centre console under the carpet behind the seats and through the existing hole the cars existing wires go through into the boot. From there it was ran around the outside to where I had installed the phatnoise box itself.
The phatnosie box I have has had its wings cut off which for an MX5 is a good thing as there aren't that many free spaces, especially if you already have an amp in the boot.
But like this it fits neatly in. I can also confirm that in the Skoda Symphony manual it does state that if you take the head unit out of a VAG car the head unit and cars ECU talk to each other and know it is the same head unit. So if you take it out of the car and then put it back in the same one you do not need a security code to get it working again. However if you put it in a new car the head unit knows its not the same car and asks for a security code! What a bummer unless you know.