I just put diamond audio Hex's in my S2000. i used the 6.5" version and did some custom adapting.
as for a sub...
easiest is the JL stealthbox that replaces the styrofoam jack/tool holder in the bottom of trunk. but then you have to find a place to mount the amp. alot of people are mounting them on top of the gas tank (to the left of the spare tire. dont be afraid to pull some panels out and look around.
some people are also doign custom sidewall fiberglass enclosures in the trunk for good sound. that way you keep the functionality of the flood of the trunk in tact.
check out the audio and electronics forum over at S2ki
http://www.s2ki.com/forums/index.php?s=&showforum=26
for lots of good info.
good luck...they are challenging cars to get sounding good. imaging for bothsides is nearly imposible. you can get one siude with a time delay...but then the other side sounds WAY off.