ladydesire posted a great tutorial on how she made custom prestige classes for Waterdeep.
Check it out here:
http://nwcitadel.com/forums/showthread.php?t=1138
Also, you may get some benefit in Kaedrin's post where he was exploring this issue:
http://nwn2forums.bioware.com/forums/viewtopic.html?topic=596753&forum=1...