hey, welcome, and nice yj. i did use the pods that go at the bottom of the roll cage, i bought empty boxes premaid to fit there, and put good pioneer 3 way 6x9's. my yj came with a speaker bar factory, so i put kenwood speakers in their place, and i had a 10" sub, with custom a box bolted down in rear cargo area and put the amps under the rear seat. i haven't been in the stereo game for a long time now, but you get what you pay for, the sound bar on top will help, but just make sure they're good speakers. the pods on the bottom will work well to with good speakers. and securing an amp and sub isn't hard, and if you're running a soft top, the top folded down pretty much covers the cargo area from the weather.
enjoy, and don't forget to wave.