While this may not be the preferred way to do this, I did it and it works to my liking. If there is another way or if someone sees an error in my steps, please let me know. Also, I have the retractable cargo floor, so it may be different for the regular floor.Thanks.

1) Remove panel covering factory subs.
2) Remove floor trim covering lower portion of sub box.
3) There is a black trim piece that covers the wires and such that needs to be removed (2-10mm)
4) You should now see the connector for the subs. The factory subs are dual-voice coil so there are a total of eight wires in the connector.
5) Remove the connector. The top row of the connection has 2 brown wires and 2 blue wires(If I remember correctly)
6) Connect the negative wires from the high-low convertor to the brown wires and the positve wire to the blue wires.
7) Run the RCA cable from the convertor to the amp
8) Run the remote turn-on wire from pin 13 to the remote on the amp
9) Run power from the battery to the power of the amp
10) For the ground, I used the bolt that holds the cover over the spare tire, I scraped away some of the paint to ensure a good ground.
11) Connect speaker wires from amp to speaker.

I had some pictures but they look less than ideal (took them with my Treo), a little blurry. If you want I can post them too.
Hope this helps.