Wendersnaven.com (a resource for nwn2 builders)

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=115