I still plan on making separate compartments but the compartments are mostly for air pressure benefits so the speakers work more efficiently.
Since a 6x9 and a sub woofer will have some audio frequencies coming from them which are the same, you need to make sure the 6x9's and Sub woofer speakers are working together. So for instance, since the sub woofer will be down firing and the 6x9 will be up firing....when the 6x9's cone is traveling outward (away from its magnet) and pushing air upwards, the sub woofer will be pushing that same air/sound downwards (away from its magnet). Think of a tug of war scenario with a rope....you basically have the same sound pulling in one direction while the same sound is pulling in the opposite direction. The net effect is that the sound will cancel out or be significantly reduced in level....thus the tug of war where the stronger sound wins but it is moving the rope much slower. Now by reversing the phase
of the sub woofers.....while the 6x9's cone is moving outwards(away from its magnet) and up, the sub woofer's cone will be moving backwards (towards its magnet) at the same time. Thus now they are working together and pushing the rope together at the same time. Where the net effect is more movement of that sound since you essentially have both teams working together and pulling on the same side of the rope at the same time. When you have them working against each other, this is known as "phase cancellation" which results in reduced volume at those frequencies that the sub and 6x9 are producing at the same time. This is where you can actually have more speakers playing, but creating less sound in the vehicle. You can disconnect the subs and actually hear MORE bass if the sound is phase canceling with the 6x9's.
To reverse the phase of the sub woofer you would connect the NEGATIVE wire to the POSITIVE terminal on the sub and the POSITIVE wire to the NEGATIVE terminal. If you have a home stereo with a separate sub woofer box/amp, you will often see a switch on it which is labeled "Phase". Where it might be labeled "0 degrees" in one position and "180 degrees" in another. The 180 degrees position does what I described above by switching the wire connections on the speaker.....well, it actually does this electrically, the result is the same.
There is no way to block the sound coming from the sub woofer so that it does not interfere or Mix with the sound of the 6x9. I think this is what you where describing by suggesting putting barriers between them and sealing them. That's not at all what you are doing when you do that.
To do what you are describing, here's what you would need to do when building a speaker box. A sub woofer will reproduce sound in the 50Hz frequency range and so will a 6x9. The "wavelength
" of 50 Hz is about 22 feet long. To stop the 50Hz sound from going through the barrier you would need 1/4 thickness of material of the length of the wavelength. So about 5.5 feet (22/4=5.5) thickness of material. As the frequency goes lower...the wavelength gets even longer. So you might start to see why you couldn't build a box that would separate the sound of the sub woofer from the sound of the 6x9. You would have to be using wood which is 6 feet or thicker to do that.
This is why when you walk on the outside of an arena where a loud concert is going on inside, you can still hear the low bass of the music playing from the outside. The walls of the arena are not 6 feet or thicker to block the sound from escaping to the outside. This is also why when someone drives by with their stereo blasting you can hear the bass from the subs as they drive by and you mainly just hear "Boom.....Boom.....da....Boooooom". You hear the bass...because the bass frequencies have the longer wavelengths. The higher frequencies have much shorter wavelengths and the walls of the vehicle will stop those frequencies from traveling outside of the vehicle. 1000 Hz has a wavelength of 13.5 inches, so material that is thicker than 3 inches (13.5/4=3.4 inches) can block that part of the sound from going through the material, going outside the vehicle and reaching your ear.
Most wood for speaker boxes is 3/4" thick....that's only really being a barrier for the audio frequencies above 4000 Hz (4Khz). A sub woofer doesn't reproduce sound in the 4Khz audio range.
Sorry for the long post....audio is kind of my specialty and you seemed a tad confused.