If you don't have Wayne's book I recommend getting it. Here are some articles from it that may be useful, if not at least for some interesting reading:
Pelican Technical Article: Boxster Muffler Replacement - 986 / 987
Pelican Technical Article: Installing a Performance Boxster Exhaust System - 986 / 987
It souds like you're not talking about replacing the headers, so if that's the case you've got a lot less to worry about than if you're doing a full system. As Ghostrider mentioned, the header bolts apparently like to snap like twigs and leave you SOL.