Steps, in my recommended priority order, cost, benefit, time to do:
-replace dash speakers w/ good coaxials, $80, add clarity, 2-3 hrs
-replace doors w/ baffle and 6.5" good woofers (or coaxials - but will only still get lows due to crossover built in to amp), $100, add better mid to low end power & clarity, 3 hrs
-add rear speakers, $250, move sound stage out from behind windshield to middle of car where ears are, 2-3hrs
All of these will keep stock appearance.
The #1 problem w/ Boxster sound system is clarity. The cheap paper cone OEM speakers do not give it to you. Most people will fire off right away and say get a new amp. If you do that w/out replacing the drivers, all you get is louder crappy sound. All can be done DIY with low/med mechanical/electronic skills. Just takes some patience and is well worth the effort. If you're not happy w/ the sound afterwards, then upgrade to a more powerful amp (obviously requires some foresight in picking speakers out. But know the OEM is 40W per channel which is pretty powerful - 60W would be more than enough if you aren't looking for bass thumping car alarm setting off sound)
Here are 2 guides to help you:
Upgrading the Boxsters Sound System Overall Guide
Baffle Template for Door Speakers
Good luck!