Cheers, I don't mean to sound thick but are you saying that I should connect the live to the earth and then connect those both to the red and yellow?
What cable should I use as a feed from the battery?
I would advise against connecting both the permanent live and accessory live to the cable you run from the battery, as your head unit will be permanently energised, and not ignition sensitive. You run the risk of getting out of the car leaving the stereo on, which will result in flat battery! I would always want my headunit to switch off when the key was removed from the ignition, which it won't do with the above set up.
Diz is certainly right that the Mk2 loom is not capable of supporting the current draw of modern head-units, and the best way is to run a cable of decent guage from the battery (fused of course) through to the head unit location.
But I would use this only as your permanent live replacement, and I would connect your accessory wire (or switched supply wire) - from your new head unit - to your existing igntion switched supply.
It is not a problem connecting your head unit in this way, as the headunit actually pulls very little current through the igintion switched live. Much like the remote wire to an implifier, it works as a switch, and only needs to be energised in order to work.