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You can build the boxes with in the CI specified on the box. 99% of the time, 6x9 speakers will perform best with out an enclosure, using what some call "free air" or "infinit baffle" The 6x9 boxes that have been so popular to put on the rear wheel wells of jeeps are enclosures, but are considered universal due to that they are not sealed, allowing the passage of air.
If you want a awesome design that I have used in other peoples jeeps (not my own only because I run rear components in fiberglass enclosures) Have the sub in the center of the cargo space, facing down with about 10 degrees of pitch towards the interior, and build to specs! Use some plywood to build a "instant trunk" and secure that to the top of the enclosure and mount the 6x9's on either side, putting shims in the rear to angle the speakers direction towards the interior. If you have a router and chisle's, instead of shims, you can remove material on the otherside if so desired. Don't go crazy with the angle's, you only need about5-10 degrees.
then make a 3 sided enclosure to put around the bottom (magnet) of the 6x9 mainly for protection and to clean up the install.
I will try to post a quick drawing of what I am try to explain.
Johnny[addsig]