Ok, this can get ugly, but I have put in the full aftermarket subwoofer set up. First I ran a major power wire from the battery to the amplifier, 4 gauge. {yeah, too much, I know} and then ran the same gauge wire to a back seat bolt down for the ground wire from the amp. Next, I installed a cheap 1000 watt amp that is actually pushing more like 300-500 watts. After bridging it to get the maximum power, I then connected it to two 10 in MTX subwoofers that are run together in parallel. Again boosting power. As for the signal, I simply unplugged the rear speakers and plugged them into the amp, no cut wires or anything.
When I first put this set up together, it was more testing the set up to see what it was capable of and preparing for my custom 12 in subwoofer set up. However after completing installation and upon further testing, I have concluded that the custom 12 in subwoofer setup would be "overkill"...Im not much of one for "head blasting bass" and this current set up can go to that point with a few different songs...Tupac's California love can defiantly rattle the windows.
As for hookups to the stock radio, none. But aftermarket systems would be your best bet, especially considering the stock radio only puts out 25-30 watts per channel. {pathetic if you ask me}