well, if you remove the stock amp, for your new headunit, you will need to rewire all of your speakers. however, if you plan on using an amp to power all the speakers, sub or not, all the wires going to the speakers are under the rear deck where the amp is. so if you were replacing your stock amp with an aftermarket, all the larger gauge speaker wires are already in the trunk, meaning they all run from the trunk to each corner speakers. in this case, you would just need to wire in your headunit to the amp, and splice the speaker wires into your new amp. it is your option to include the sub with this amp, as its already wired into both rear corners, or if your headunit supports, you can use a seperate amp to power the sub to control both amps, or rca them together.
not sure why you need an output after your sub.....? you only need the line output converter if your using rca from the headunit harness. if you use your aftermarket headunit, which should have rca on them, you just run the rca to the amp, and wire in the head unit, and youre good to go.
it doesnt matter, you will need to add an amp turn-on wire if youre using an aftermarket amp. normally you can follow your rca with the remote turn on, these wires should be opposite side of car as your power wire.
from my understanding, you want the stock amp to power all the speakers, which it already does. so you can just wire in your headunit harnesses. however, if you want to add another amp, you will need to wire in, or double, the amp turn-on for the aftermarket amp, and plug the rca for the aftermarket amp into the headunit itself, not the harness with rca. if you want it to power the stock sub, just cut the wires and wire them into the new amp if youre not adding a new sub.
the sub is already wired into your preexisting setup, it is part left rear, and right rear corners. there is no premade harness for this, the sub only has 4 wires, follow the wires back to the stock amp, cut them, and wire them into your new amp. all the wires are different colors, you can find the color codes in the fsm.