I have ModPods under the doors and sound wedges for 6X9 speakers on the rear. Those two mods will improve sound drastically.
ModPods:
Sound Wedges:
Both of these pics were taken about 5 or 6 years ago, but these same components are still in there... As for the cup holders on the sound wedges, don't try placing bottles there; they will not stay there even on the road, much less off road!
Like Jeffy said, the stock location is not optimal for good sound, so if you plan to invest in your sound system, might as well relocate it to improve the sound quality. Just make sure you use plastic cone speakers for the ModPods if you expect them to last (mine have been underwater and undermud a couple of times and are still alive).
As for the sub, I run a 12" aluminum sub with an amp, but now a days, you can get the super slim subs and even make a box for them under the rear seat so you don't loose any space (there are a couple of threads on how to do this). You can also use the stock TJ location if you choose, but I would go for a 10" instead of a 8" if I were you.