I do not recommend Boss at all. They are a low quality manufacturer who slaps big numbers on their products that can't back them up. A "1000 watt" subwoofer from them will likely only handle around 200 watts of true continuous power before the cone blows out and your Jeep fills with smoke. I would go with a well-known brand; Alpine, Kicker, Polk, JL, etc. You really don't need a ton of power to fill the cabin of a Jeep as long as you pick the right equipment.
Figure out where you want to put the sub(s) first. Space limitations are often concerns in Jeeps, but your Unlimited should have plenty of room; if you don't need to do a shallow mount sub, don't. Shallow mount subs work in very small enclosures, but the sound IS affected. You should have plenty of room for one or even two 12" subs if you don't mind giving up some cargo space. Once you figure out where you want to put them, and how big of an enclosure you can fit, you can pick out the sub(s).
There are two main things you will want to look at when picking out subs. First is the continuous power handling, or RMS power, and the second is the nominal impedance of the sub, measured in ohms. Manufacturers will often put two ratings on their products, max power and rms power; the rms power is usually around half of the max power, and is what you want to pay attention to. Also, some subs are single voice coil, some are dual. Each voice coil has it's own impedance, so a dual 4 ohm voice coil sub will actually wire down to a 2 or 8 ohm final load into the amp. My old Alpine Type R sub was a dual 4 ohm sub that handled 600 watts RMS (300 per voice coil).
After you pick the sub, you will need to get a box for them. Some subs are sold pre-loaded into an enclosure, usually designed specifically for that model sub. Other subs are sold as just the sub, leaving it up to the consumer to design and build a box, or buy a pre-fabricated box to drop it into. Unless you want to build your own box, I would suggest looking at pre-loaded enclosures - Kicker makes quite a few good ones for nearly every budget.
Lastly, pick out the amp. Again, you will want to look at the RMS power output - not the peak. Also ensure that the amp is stable down the the impedance of the sub you want to use; if you buy a sub that runs at 2 ohms, make sure the amp is 2 ohm stable. The lower the impedance (ohms) the more power the sub will pull from the amp, so you will often see amp ratings like this: 400 watts RMS x1 @ 4 ohms, 800 watts RMS x1 @ 2ohms. This means that if you wire a 4 ohm sub into it, it will provide 400 watts to the sub. If you wire a 2 ohm sub, it will put out 800 watts to the sub. Match the wattage as closely as possible without going over the subs rated handling.