They are taped up into the central locking loom as that piece of loom goes to the tailgate.

You run the whole lot down the left side of the car, over the near-side rear arch. The plug for the speakers will pop through a cutout on the left-hand parcel shelf support (bottom wherei t meets the boot trim) and then the central locking loom should go up to the roof where it goes through into the tailgate aperture.

It will not affect the alarm in the slightest as it is only routed with the central locking wires, and is not in any way physically connected into that system.