Honestly, that ebay option is your best bet. Finding the right wires to splice, and then doing so w/o interference will be a MAJOR pain in the ass.
That being said, there's no reason to put subs in a jeep. With the hardtop the bass hits REALLY hard. I have a small 60W 10 inch, and even that is hitting pretty decent.
Infinity Basslink Subwoofer Install - Info & Pics
See there,
and here's what you'll need.
Scosche SLC4 Four-channel line output converter at Crutchfield.com
Now are you trying to add subwoofers to the existing system or replace the existing subwoofers? If you want to add them (w/ there own amp), then the easier thing is to look for the amp (not sure in JK) and find a bundle of four wires (2 blacks and then two same colored w/ one striped) figure out what ground is to what colored wire and then splice into the four wires with quick splice clips. Run those wires to your line level converter (MAKE SURE TO GET THE BLACK WIRES CORRECT), and then output that to your amp.
Like I said, I don't know too much about the JKs and firewall location, just
be sure to run power one side and audio cables the other. Interference in these cars is nasty.