I think running wires directly from the amp to the speakers is "neater". As for how to run the wires...it all depends on where your amplifier is.
If you're putting it under the passenger seat: for the LEFT FRONT speaker, I would suggest going up into the console, that will run you to behind the deck, where you can easily go under the steering wheel and into the door. The best way to get to the LEFT REAR speaker is to go up through the console but cut back under the carpet right behind the driver's seat. That will get you to the door. For the RIGHT REAR speaker, do the same as for the left rear but on the opposite side and without going through the console. and for RIGHT FRONT you would do the same as for the left front speaker, except go the other way when you get behind the deck.
The easiest way to run the speaker wire under the carpet to the rear doors is to take the bottom part of the back seat (the part you actually sit on) and pull some of the carpet back. Then feed the wire to the back, then to the door(s). Once you're at the door, use JOHNE's suggestion for getting your wire there. But DEFINITELY use new speaker wire.
It's all pretty simple, just takes some patience. Oh and if your amp is in the back, you can get to the doors the same way you got your amp wires there.
