I wanted to make a complete list of references I used in order to complete this installation as well as address some questions I had and why I made each decision. I am by no means a professional, but I do think I made the best decision for my needs and hopefully this helps some others if they decide to upgrade their sound system.

Subwoofer Choice
The two biggest considerations on what I wanted was: no impact on usability of the cargo space and ease of installation (no external amps).
These requirements narrowed down the list to powered subwoofers that would fit under the passenger seat or a spare tire subwoofer.
My options were:

• JBL BassPro SL 2 / Infinity BassLink SM 2(Pretty much the same thing) 8" 125W RMS ~$350
  • Decided against due to reviews stating they might be underwhelming. I wasn't looking to rattle the neighbors windows, but if I'm going through the effort of doing this I should get a noticeable improvement.
• Kicker 46HS10- 10" 180W RMS ~$320
  • The clearance under the passenger seat is very small. In this video, the aforementioned BassPro SL2 is installed with barely enough clearance at 2-7/8" tall. At 3-3/8" tall, there is no way the kicker would fit without removing the rear seat vent.
• JBL BassPro Hub- 11" 200W RMS~$500
  • One of the more popular options. Most expensive option but possibly also the best option.
• CERWIN Vega 600 watts Active Spare Tire Application Subwoofers Series (VPAS12ST)- 12" 150W RMS ~$340
  • The option I ultimately decided on. Had never heard of Cerwin Vega until a co-worker brought them up, but it seems like a good option. Being cheaper than the Basspro Hub made this my choice and so far, I am happy with this decision.

Parts list

Cerwin Vega gives clear guidelines on what power cables to use for the installation. Oxygen free copper (OFC) is required, getting the cheaper copper clad aluminum(CCA) cables will void your warranty. Manual

• Speaker wiring kit- This is a good quality kit. 8 Gauge is probably overkill, especially with how short our run will be with the battery in the trunk, but I followed the manufacturer recommendation. Very problem free, you could probably shop around and save some money here. I did not need all of the power wire, but a kit with pre-terminated ring terminals and a high quality fuse holder was exactly what I was looking for.
• 20 Amp Fuses- The wiring kit comes with a 60A fuse, the manual requires a fuse no larger than 20A
• Butt connector- The heat shrink cover is great, only needed one for the installation.
• Posi-tap- Used to tap into the speaker wires on the B-pillar. Recommended over the cheaper t-tap due to t-taps possibly cutting wires.
• Sound deadening mat- Not required, mostly got this for peace of mind in case something might rattle with the subwoofer installed.

Installation
Here are the main references I followed for the installation.
Cerwin Vega Manual
Install
Install pt. 2
Forum post on correct speaker wires to tap into
Key differences from the video installation:

• I would not recommend under any circumstances tap into the rear cigarette lighter port as shown in the video. If you have the hybrid, the battery is right next to you. If you don't have the hybrid, follow the same setup as every other car, with the power cable running through the firewall of the vehicle. Do not tap your subwoofer off of a 14ga power line.
• I did not remove the rear seats. Pulling up the flaps in the cargo area and removing the bench seat cushion is more than enough to route the wires.
• I did not have a convenient ground to the frame like the TRD adventure in the video, my ground connects directly to the battery.
• I did not remove the rear quarter panel

Concerns

• Power draw: Unlike a conventional ICE, the 12V battery in the hybrid is not charged by an alternator, this means you cannot simply slap in a larger alternator. This thread discusses the maximum safe power draw for this vehicle. The figures reported for this subwoofer are inconsistent, but the manual states 150W RMS power draw. TLDR: as long as you stick with one of these subwoofers, you will be fine.
• Bass roll off:This is a concern I have seen in some posts, and exists to extend the life of the OEM speakers. At high volumes, users have reported a falling off of the sub bass frequencies and this seems to be inherent to OEM headunits. *edit: after further testing this does seem to be the case for the pioneer system as well. This can by addressed through the installation of an LC2i output converter, but I will not be doing this at least for the moment.
• Only high level input from passenger side rear speakers? From my research, subwoofer signals are a mono signal and not a stereo signal. Some forums indicate that having both sides would be better, but I haven't noticed anything wrong with my testing.
• No remote turn on wire? This subwoofer has an automatic turn on circuit on the high level speaker input. When the door speakers get a signal, the subwoofer will power on and vice versa.