The main thing you need to look at is where the subwoofers amp is getting signal. If you want to use the stock headunit, your going to have to use something like this:
Scosche LOC80 2-channel line output converter at Crutchfield.com
You would wire this device in line with a door speaker, ideally this installs an output for the subwoofers signal. From here you would install the rest.
If you install the Jenson headunit, it may have this output available on the back of the unit and you would not have to buy a output converter.
You may not like the look, but the functions and features are nice to have.
Let me know if you need any help. I installed my setup.