5-speed and 6-speed axles are different - 6-speed is a longer transmission and requires longer axles. the 'S' model also had wider wheel bearings. also, things changed in 2003 - i think they went to the wider bearings on all models, but the 5- and 6- speed length difference remained. for a 2000 S i'm pretty sure you can use any 6-speed axle from 2000 to 2004, but nothing from a 5-speed.
edit to note that you can confirm by checking part #s; here's an online source:
http://www.********************************************.com/porsche-parts/986-97-04/porsche_boxster_parts.php