6x9’s stock or aftermarket enclosure?

Try to work your system up so that the front speakers couple with the subwoofer to provide the bass response.  The rears are best used highpassed with very little apparent bass response...the sound should just be loud enough to provide more presence to the front soundstage.  If the sub is located in the trunk, the pressure it creates will whack the 6 X 9 cones because the air pressure is seeking escape through the membranes of the speakers.  The baffles described above help to alleviate this pressure but are not designed to completely seal the speakers as a constructed box would.  And, sealing them is not what you want to do anyway as they should be mounted infinite baffle.

If you provide an air passage from trunk to cabin to allow the sub pressure to equalize throughout the car, the pressure on those rear speakers will diminish.  Do that along with baffling the rears.