hello mate, i cut the originals at the iso block round the back of the stereo on mine, and then ran new leads to the amp from the existing wires, just to be lazy, but if you want to run new wires, you can, you just have to take a bit of time to get the door card off and everything and fiddle around with feeding the wires through the gromet (I think a little modifying may need to be done to get in the gromet, i cant remember)
I did do it on my mates clio for him cos he wanted al new wires!!!
the other alternative is to just drill another hole next to the existing gromet and run a new gromet with the new wires only in it!!!!
Probably the easier way to do it providing you leave enough wire for the door to open fully!!
Liam