Be careful if you buy a carpeted box and leave the top down a lot. My biggest problem was not theft but rain. If water of any kind hits the box, the partical board will flare up and fall apart. The best option would be to take the carpeting off then paint the box so it's sealed then re-carpet it if you want it more weather proof. Otherwise you could have it recovered in vinyl.
If you're keeping your rear seat and you occasionally have 3 other people in the Jeep, you might want something smaller then a dual setup. What little room you have will be reduced significantly. If you go offroad, you will want to make sure it is secured or else removable. Also make sure your amp is located in a place where it won't get wet or just mount it to the box and remove it too. Water collects at the lowest place so under the driver or passenger seat isn't a good place. Not to mention it's not very flat there.
One thing that hasn't been mentioned is what type of music do you listen to. This will really dictate what type of speaker and box design you should go with. Also, it's preference...
Types of boxes
Free Air - subwoofers are either mounted under the rear deck or behind the rear seat of a car. This configuration will not work very well for hatchbacks. Holes have to be cut where the woofers are to be mounted. Since the woofers use the whole trunk as a box, the trunk has to be as sealed as possible from the cabin. Trunk can be isolated usually by putting particle board under the deck and behind the seat.
The drawback of free air subwoofers is that bass will not be very accurate (especially at lower frequencies), and more amplifier power will be required than with a regular box, but then again, you still have a full trunk
Sealed - is the most common box and easiest to build. These boxes will give the flattest frequency response, and best overall sound quality (especially at lower frequencies). The box internal volume should be as close as possible to the recommended by the manufacturer. If a box is smaller than what it is supposed to be, the sound will be tighter, but more amplifier power will be required. If the box is too big, then the sound will be muddy.
Ported - boxes are usually bigger in size than sealed and have a "tube" (port) that lets some air out of the box. The idea of a ported box is that the speaker port pushes (or pulls) air at the same time as the woofer, reinforcing bass. The box itself acts as an amplifier, yielding to more bass than a sealed enclosure (3 to 4 dB). Ported boxes do not have a linear frequency response. If the box is not built according to specifications, it will not sound good. The box design acts as a filter, cutting off lower frequencies.
Isobaric - configuration is a good way to get bass in a smaller box. This is done by building a box about half the volume of a sealed box, and placing two woofers facing each other. Note that everything must be sealed, including space between woofers. A spacer between both woofers must be used in most cases to avoid subs hitting each other. When wiring, make sure that woofers are out of phase: Wire one of them backwards (negative to positive, and positive to negative), so that both pull or push at the same time. An isobaric configuration will NOT put out much more power than a box using a single woofer. Its main purpose is to reduce box size. Another drawback is that since one of the subs is exposed, it is more prone to damage.
Band Pass - enclosures consist of a woofer between a sealed and ported box. Bandpass boxes will yield more bass than sealed and ported boxes (especially at lower frequencies), but over a narrower frequency range. Since the box acts as a filter, mechanically blocking lower and upper frequencies, a crossover is not needed in most cases. These enclosures are usually big, and very unforgiving when precise volumes and port sizes are not followed. Bandpass boxes also tend to mask distortion. If you can't hear distortion and turn your stereo down in time, you could damage your subs.
Aperiodic - Very small boxes that "breathe" through a moving membrane. Both the membrane and cone can not be in the same exterior space. Either the membrane part has to be isolated by cutting a hole in the car so that it is outside, or the subwoofer has to be isolated from the rest of the trunk in a similar fashion to free air woofers. The "box" has to be as small as possible (ideally the membrane should be right up against the sub), since it is used only for coupling the sub and membrane. Aperiodic membrane configurations are very hard to design and tune, but give good frequency response and respond faster to transients, giving accurate and tight bass as opposed to boomy sound. They are not ruled by Thiele-Small parameters like other designs, so any woofer would work with the membrane.
Also make sure you get the right sub for your setup. Some are designed to be used with a certain box type. You will also want to check the specs on the sub to make sure the box is the right size for the sub. Subs are designed to run optimally with a certain size box.
If this is your first time going with amps, do a little research on them also. Make sure you compare apples with apples. Some cheaper amps will list their Peak wattage because it's usually much higher then the RMS. RMS is the peak sustainable wattage the amp can produce.
Then there is the question on if you want 'rear-fill' speakers or not. Rear-fill are rear speakers. If you don't have 3 or more people in the Jeep any any one time, rear-fill isn't really necessary unless you really like rear fill. Otherwise concert style with all the speakers up front will do. Keep in mind that the stock front speakers are pitiful. Even if you replace them, with better speakers, they aren't going to be that great. If you want better sound then it would be better have some 5.25" or 6.5" speakers mounted elsewhere. There is a company that makes a small pods that go on the floor below the doors. This is probably the furthest place to mount them without getting into the pedals. This has to do with the sound imaging. You want the left and right to be equal distance from you. The further you mount them away from you the closer they are to being the same distance.
Another thing you might consider is running separate tweeters up might some place. Also, you'll want to 'cap' the other speakers. This will cut off the bass to them and will make them last longer. Caps are capacitors. You can find ones designed to be used with speakers. Otherwise you can go to Radio Shack and buy the right cap. Problem is you need to know what size cap will filter what part of the frequency. I'm sure there is a chart online someplace for that too. The ones that are prepackaged will have a frequency range listed on them.
Wow, that's a lot of stuff. I've been through 2 receivers, +10 speakers and 3 boxes so far. I want to eventually redo the whole system though. Probably custom mount everything this time.
Oh and keep in mind that if you have a soft top, you won't get anything close to decent sound. You'll probably get lots of highs and a bit of bass but muddy mids at best. Bass out of a open top or softop won't have much to bounce off of and you'll want more just so you can hear/feel it. Problem is everyone else will be able to hear it too.
The difference between the Bazooka's. Really to be called a Bazooka, it's got to be made by SAS. They have several models. The cheapest is the single coil. Then the next model up is the dual coil. Then they have the powered tubes. They have a 100w and the 200w bass tubes. The difference with the Marine models is that they are UV and moisture resistant so they can handle a bit of rain and lots of sun better then the regular models.
For those with subs already, make sure you dust the sub off occasionally. Dust will pull moisture out of the speaker membrane and cause it to dry-rot. (I've had to fix a few tears in mine.)
