if they are 9V then you obviously need to bring the 12V down to that. that can be done with a voltage divider but that involoves mucking around. i set up computer speakers in my very first car (corolla). just chopped off the 240v transformer (cos they were 12v comp speakers) and wired in to the cigarette lighter. then wired the front channels from the head unit in to a 3.5mm plug which went in to the sub/amp and from there the speakers plugged in to that.

what i found was you had to keep the volume quite low on the headunit and use the speakers' volume control to turn it up and down. get some wicked clipping if you crank the headunit volume up

pre-outs would be the way to go. just get one of those rca-3.5mm (or whatever input you have on the speakers). that would probably stop what i experienced but i only had the stock toyota hd.
personally, i would make some speaker boxes for 6x9s/components cos i hate having shit sounds
