Essentially - whatever's the easiest (and still provides good quality).

In my VW Polo there were prewired componet speakers in the doors (front only - it's a compact hatchback). At the A-pillar, where the rubber tube leading to the door is, there's a solid plug with connectors for the wires in the doors. To run new wire to the door speakers I'd have to locate unused spots in the connectors and drill through, or drill new holes in the mateal of teh door and pillar and use a new rubber tube - either way a major PITA.

As I run no extreme amount of power, I decided to use the stock wires, so I ran the amp speaker outputs for the front speakers to the connector in the dash behing the HU.
If there hd been nothing blocking access through the rubber tube, I would probably have gone with new, somewhat heavier gauge than the stock, wires.

I replaced the original flimsy rear shelf to add speakers there. As there was nothing prewired for rear speakers, I ran directly from the amp (though via a connector so I can remove the rear shelf if needed).

/Michael