2 harnesses...good choice. Then you don't have to:
1) do the grunt work in your car and
2) risk messing stuff up/shorteneing the factory wires.
I should have taken a pic of my system when I put it in. Anyhow, I took the two harnesses and cut the wires so that they were about 8" long combined. I altered the length so that all of the "crimps" wouldn't be in the same area, and then I soldered and heatshrink wrapped mine.
I've done it several times just crimping for other people, and it seems to work fine as well. I prefer solder when I'm working on my own stuff, though