Since the amp is built into the box with the sub, youll have to get power, ground and signal to it. Ive never seen one in person before but youll have to figure out where it should get power from, weather from the radio itself or if you will have to run a line from the battery. Im sure the circuit for the radio probably wont be powerful enough so youll probably have to run a line from the battery. It also may need a ignition source to kick the factory amp on and off with the truck. Then you have to get audio signal from the radio, which probably wont be easy. And you have to figure out how to mount it and hide all the wiring.
And last but not least, im sure the sub/amp doesnt have traditional terminals to make connections to, such as power, ground, remote and so on. It probably went into a toyota specific harness that plugged into the amp, so youd have to come up with a way just to make connections to the thing.
In the end, it will be ALOT of time and money for really no improvement over stock. There are a bunch of designs out there for small sub boxes that keep use of the back seats and compartments that sound great, and dont require cutting the truck up like you will have to to put a factory sub in there.
EDIT: Actually I just looked at the factory sub/amp setup in that link, and yes it is all powered by a special connector. It wont be fun to try to make connections to that thing.