There are a couple ways you can go about.

1st run a continuity test and verify that you have a short.

2nd follow the wire from the speaker mount till it enters the cabin, wright down the colors of the wires for the right and left side. Then pull the stereo remove the (speaker wire only) your replacing from the harness . Then its a matter of runing the new wire to the speaker mount and wireing them to the harness.

Or install an amp much better then screwing with the wiring harness, less chance of screwing up your electrical. Both are pretty easy though.

How old is your car? Its hard to get a short in your speaker wire.