Alright, if you still have the factory amp in, I would remove that, remove the entire rack that holds the factory amp. Unhook the compass and all that cell phone crap if you have it. Just unplug all of it and get it out of the way. I'm sure you know if you're going North, South, East & West. The phone don't work anyway and the factory amp sucks.
Ok, for the inside, I would get a 6-channel amp for the four 6X8's and tweeters.
Keep the 2-channel for the subs if you're happy with it. Use the 4-channel amp you already have for the rear deck lid. I would run either 0-gauge or 2-gauge wire all the way to the trunk into a distribution block that has 4 outputs on it for either 4 to 8 gauge wire connections. The block should have an input on it for 0-2 gauge wire. Ground all amps in the same location and the rest is simple, except cutting through the metal.
I have completely cut the entire metal piece out of a car before and bolted in a 1/2" plywood piece that was cut out to fit. Speaker holes were already cut out also but with the Mark, I would just cut the metal if possible. Either a jigsaw with metal cutting blades or a reciprocating saw. Put some goggles on and lay in the trunk and keep your mouth shut. It won't take long. Make sure to measure and mark correctly. Once the metal is cut, put your top layer back in and mark it from the underside and then cut it out and you're ready.