Torque boxes are the mounting points on your frame for your control arms. The problem with them is that they're usually fine for your average daily driver, but once you start abusing it, the factory spot welds pop once they've been exposed to repeated hard launches and downshifts. I'm sure there's quite a few people here who are definitely experienced with the woes of the factory torque boxes, and maybe even some who have replaced with battle boxes, or re-welded and reinforced their factory boxes. The best way to check (and biggest pain) is to remove your rear seat bottom, scrape out the insulating material, see if the spot welds are popped, and the floorpan dented upward. If they are, plan on using a big hammer and a block of wood to beat the floorpan back down in order to re-weld them into place. It sounds worse than it actually is to fix, but plan on doing a fair amount of welding (preferrably the entire seam, not spot welds), and look into reinforcing them with some pieces of steel. A quick google search for torque boxes will probably give you a better definition, and might offer some better ideas on how to go about repairing/reinforcing them if they're damaged.
-Matt