Set a walkable path and THEN bake. Baking will "Bake" in the changes to the walkable mesh data. If you have set an area that has a placable above it that will be taken into acount during the baking process.
Its pretty strieght forward. This didnt take more than 5 minutes to learn and get this far, I realy should have earlyer because it is proving to be much more fun than NWN1 (That rymed?)
I have made some other area's one of which, well, actualy many of which will bring a tear to your eye... Sigh...