Part III:
In your 4runner (2003) JBL system, you have a 6x9 woofer and 0.75" tweeters in the front. You also have a tweeter on top of your dash (to provide a center channel). The rear door speakers are around 6.5" and they are coaxial (woofer + tweeter combined together). The cargo area has a 6.5" woofer in an enclosure which acts like a mini-subwoofer.
The 6x9 woofer in the front can produce a lot of bass. In general, 6x9 size speaker provides more bass than a round 6.5" speaker. However, it is not as efficient as a round speaker and not as clean sounding. However, again, it can provide more bass. In the 4Runner, this is why you hear most bass up front...thanks to your 6x9 speakers.
The rear speakers are for rear fill only...thus, you don't hear much from them.
The 6.5" subwoofer in the cargo area provide adequate bass for the REAR passenger. It is NOT meant to provide pounding bass to the front passenger. Why?? Because, the front passenger ALREADY has a good bass-producing speaker (6x9 woofers). Since the rear passenger is far from the front speakers, some bass will not be strong enough to reach them...so the rear cargo subwoofer makes up the difference.
BTW, the 6.5" subwoofer in the cargo area is tiny when compared to aftermarket stuff. But, as described above, it is not meant to provide pounding bass that can be heard 10 cars away!
The above setup by JBL is similar to most other quality factory sound system (Infinity, Mark Levinson, BOSE, Harmon kardon). In the Lexus GX470, Mark Levinson engineers further clarify the sound up front by adding a mid-range speaker (2.5"). This leaves the bass to the 6x9 speakers and high-frequency to the tweeter...everything else (mainly, vocals) is handled by the midrange speaker. Therefore, clarity is improved.
NOTE: the above discussion is ONLY valid if your JBL system is OK.
Hope this helps.
