The JBL system is okay, but really lacks in real bass. You'll probably want to disconnect the center speaker, most people find that it helps with the imaging and gives it a bit more clarity. It's very easy to do, just pull up on the speaker grille (it just lifts out) and un-plug it.
For hooking up an amp you'll want to use the rear speakers as the source because the front speakers are digitally equalized, so the tweeters and woofers are running as separate channels without full range audio. The rear speakers have passive crossover components and get full-range audio, so running it through an amp works well.
I helped my friend install equipment in his Prius, you can check out some of the picture in the Share section, we aren't done yet -- it's a work in progress.
We replaced the front tweeters (stock ones are a bit muddy sounding) and had put replacement woofers in, but they has some strange harmonic distortion and lacked bass so we put the stock woofers back in which sound fine but could be better. The problem was likely the stock plastic spacer, so we'll try again using proper MDF spacers when we do the next round of modding and upgrading.
Amps are really easy to wire for power because the battery is right next to the storage compartment (on the right in the Prius II and on the left in the Prius I) and the Prius has a 100 amp power converter (electronic equivalent to an alternator) so there's actually quite a bit of 12v juice to play with.