OK, a couple of things... I am work in the Audio Products divition for Sony Latin America, so I guess this I do know a bit about.
If you plan to run only 4 speakers, I would not suggest an amp. If you plan to ad a Subwwofer, then get an amp, but only for the SW unit. In my case, I made a mount for my amp so that I can take it out from under the driver seat when I go wheeling by taking out only one screw (plus removing the 5 wires for power and signal, and removing the fuse so that I dont short everything out with a live wire wiggling under the seat!).
In my case (94 YJ), I used the sound wedges from Quadratec for the rear speakers, and relocated the front ones with Mod Pods. As for the wire, I just rewired everything, as the wire that the previous owner had used for the sound bar (which I eliminated) was pretty bad. I, like Happy024, used thermal shrink tubings on ALL connections (I used the waterproof ones just in case) and soldered all splices before doing that.
I would recommend getting some good wire (as many strands as you can get, and as thick an insulation you can get for 16 AWG) for the speakers to reduce interference. If you want really good audio quality, you will need to stuff the sound boxes with the fabric they bring (they just do not bring NEARLY enough to make any effect; get about 5 times as much as they bring, and stuff it before installing the speakers. Now, one comment on this: this is for sound QUALITY, not power. But given all the noises ussually present in a Jeep, you will most likely not be able to hear the difference, so keep that in mind. In my case, I had the stuff laying around, so I used it, but I dont consider it a priority for a Jeep.
DO make sure the boxes are installed nice and tight. Otherwise you will have vibrations, and that will sound pretty bad. ANyway, if you need any help on this, let me know and I will be happy to help you...
Felipe