I just installed a 4-channel amp and put in all new speaker wire to all four speakers, so hopefully this is of help.
for my 97 accord, I actually took a small knife and made a vertical cut about three inches long in the rubber boot. most of the wire is protected by shrink tubing so it really doesnt matter if there's a hole in the boot or not. this makes it much easier to feed the wire through the boot.
from there, i just fed the speaker wire from inside the passenger compartment up into the boot, then reached in the hole I cut and pulled it up through the boot (tedious, i'll admit).
at the door end of the boot, there will be a wiring harness for the wires that go to the power windows and locks. you should be able to feed the speaker wire into the door through a small hole along the edge of the harness. then it's pretty easy as you can then reach into the door and pull the wire out through the speaker hole in the door.
hope that's of some help to you...good luck