I can help a little...
Hey, I have/had the same questions....I have a 2003 XLT with the premium sound and subwoofer. I am in the process of switching it out as well.
I learned the hard way that the panel that covers the sub in the rear is just a facade...the panel does NOT come off. I learned that by being an idiot and trying to rip it off when it fact it is "welded" to the rest of the trim panel. And oh, by the way, they don't sell the cover either, you have to replace the entire rear trim panel to fix :fire: Anyway, the only way to get to it is to remove the entire rear right trim panel. The sub itself is an 8" with a small amplifier right next to it. The space in there is pretty shallow, I really don't think you are going to get a very large or decent quality sub to fit behind the standard enclosure....you would not get an enclosure back there anyway. The sub is also bolted from the rear to the quarter panel, so to get it out you have to have access to the rear of the sub (you can get to it with the trim panel removed).
I would replace the factory amp to power any new sub you install...the factory one isn't going to be high quality and it uses a harness to connect to the sub from the head unit, so you would have to splice the wires to attach any aftermarket sub. By the way, you will also lose the factory sub if you upgrade your head unit, because the factory head unit uses a separate connector for the sub that won't exist on the new head unit.
I don't know if the factory headunit powers the satellite speakers or if there is another amp that does that (or if the same amp that powers the sub powers the satellites....but initially I had the factory speakers replaced and left everything else alone and the new speakers still sounded halfway decent.
So far, what I have done with my EX is replaced the factory speakers in all four locations with Infinity Kappa's (factory size is 5 x 7 by the way)..and switched out the factory head unit with a Pioneer DEH-7600MP. So far so good...just need to figure out what to do with the sub and some amps and I will be good to go. I think I am going to rip out the factory sub and put some kind of custom enclosure in that area (not inside but in front of somehhow) I don't know...should be pretty simple, so far nothing too complicated.
I've had the EX torn up quite a bit so if you need any help with door panel removals, etc..let me know. There doesn't seem to be a whole lot of information out there on Gen 3 explorers.