OK, I know a bit about this subject... First some background. I have worked for Sony for the past 9 years, and was in charge of Audio Marketing for 8 out of the 9. Now, 2 12" subs is A LOT of base; if that's what you want, it's fine, but one is more than enough to get good base sound. Also, most main units put out enough power (ussually around 52W per channel) to drive 4 goodsized speakers (6X9 or smaller).
Now, if you plan to run the 4 stock speakers PLUS the sound bar, I recommend a 4 channel amp; but the best sound will come from relocating the speakers, using better units (3 or 4 way with better frequency response), and using larger speakers (a couple of 6" and a couple of 6X9" would be ideal) in addition to the sub (or subs).
The sub itself will also affect the taste of the sound; I run a 12" aluminum one in my YJ with a 1000W amp, and I run a polipropilane (sp?) one with a 1200W amp in my DD (Toyota Fortuner; very similar to a 4Runner), and the sound taste is very different (I like the YJ sound better). I recommend either composite or aluminum for the sub, but that's because of sound taste preference (equivalent to suggesting which color is better for a Jeep!).
Anyway, good luck with your project!
Felipe
PS: I am assuming you are changing the head unit, which I REALLY recommend you do if you are investing in amps and subs...
