OK so I've been busy modifying and adding to the existing JBL sound system for my highlander, and I think I am done with the install/modifications (except maybe tweeters up front

) Anyway as a quick summary of what I did, I added 2 6x9's in their enclosures, an 8" sub, and sealed up every door panel and tailgate....and now to explain more in depth.
Sealing Doors/Tailgate:
The first thing I did was seal up the doors and tailgates to be more air tight. The JBL system uses the doors and tailgate as a sealed enclosure for their speakers and sub, and they are not at all sealed, which means lowered sound volume, bass response, and sound quality. So I took all four 4 door panels and the tailgate panel off and went after it with gorilla tape (a little more moisture resistant that duct tape).
The doors are sealed (somewhat) with a plastic cover, over the openings, but it had large gaps in the plastic that allowed air out, so I sealed those holes with tape and any loose parts around the edge of the plastic, so that the only place air could come out would be the weather stripping around where the windows meet the door frame.
The tailgate (once the plastic is taken off) isn't even sealed with plastic. The fact that the subwoofer's enclosure isn't sealed was pretty ridiculous considering how important that is to a sub. So I used an entire roll of gorilla tape to cover EVERY hole and opening, except for the push pins holes (there are a TON of them). So after doing all of that and putting the door panels back on, the speakers definitely had a little more kick to them. The improvement to the subwoofer was even more extreme, as it now actually had a sealed enclosure to work in. It has more volume at lower frequencies which is great. So for anybody with the JBL system (or even the base radio for stock speakers or replacement speakers) sealing up the doors and tailgate are a pretty easy and cheap fix (2-3 rolls of gorilla tape 4 dollars each at walmart).
Additional Speakers/Sub:
Now for the rest. I wanted to add to the JBL system not replace, as I wanted any upgrades to not mess up the system and be transferable to any new vehicle. So I started with getting a pair of Pioneer TS-D6902R and putting them in a 6x9 enclosure and mounting them in the trunk.

I had hoped that they would add a little more bass to the system while adding to the mid range sound from the rear of the car. The stock 6.75" speakers in the rear doors distort heavily with any low frequencies. These new 6x9's helped with some but not as much as I wanted. So I tried to port the 6x9 enclosure and tuned it for 50hz. I am powering these speakers at 50 watts rms each with a Dual XPA2500 amplifier and have the high pass filter set at 60hz. Now these speakers hit some low notes, but not too low that it distorts the mid range sound. But I still wanted more bass

So I started looking at 8" subs. 8" subs provide a punchy bass rather than the booming sound of a 10 or 12 inch sub. Plus the stock JBL has some bass to begin with so I wasn't looking to add overpowering bass. So I got a JL Audio 8W1v2-4 sub, a Pioneer GM-3400T and a Sound Ordnance 8" sealed enclosure. The great things about 8" sub's is that the enclosure's needed are very small (as seen in picture). I wired it up running right at 150 watts RMS, and have a low pass filter at 80hz. It adds a lot of bass to teh car when the radio bass boost is up and speakers are maxed, but not enough to over play all the other sounds from the speakers. It has plenty of bass to rattle the cars and windows. Everyone's idea musical sound is different, but with the 8" JBL stock sub, the 2 stock 6x9's in the front door (mostly bass), and the JL 8" sub, this car has plenty of bass. And with the addition of the 6x9's it sounds great. When in the drivers seat the sound comes from everywhere (not just in front of you) and is much fuller/richer. Though the new 6x9's tweeters really make me realize how much the front is missing high frequency sound.
Amp Install locations and wiring techniques:
Now for the amp install. The Dual XPA2500 (speakers) is mounted under the passenger seat:

The Pioneer GM-3400T (sub) is mounted in the foot area of the 3rd row on the driver side:

All the wires are run along the edges of the car under the plastic trim panels. I tapped into the rear speakers (after amplifier) + lines for the high level input. The Toyota head-unit outputs sound signal and volume on two separate wires so you have to tap after the amp to get volume changes to work.
I've read on this forum a few times people asking where to run a power line to the battery through the firewall. Luck123 explained where to find it in his sub/radio install, I'd thought i would put a picture to his words.
In the passenger foot-well (after removing the black AC cover that hides everything down there) there is a rubber grommet that runs through the firewall. There is a 3/4" band of wires going through it. Below the bundle (about 1cm, still part of the same rubber grommet) there is a plug looking thing. It is actually another hole to run wires. If you cut this plug off using a razor blade or scissors there will be a hole into the engine bay you can run power lines through. I ran my 2 8-guage power lines for the amps through this hole.
Additional Information
Front Door Panel Removal Guide
Rear Door Panel Removal Guide
Tailgate Panel Removal Guide
(Picture were taken with a camera phone, so they are very fuzzy sorry haha)
Hope this helps anybody thinking about audio modification.
Patrick