The arm navigation wizard uses the new environment server code released with electric. This tutorial explains in detail how the environment server works:
http://www.ros.org/wiki/arm_navigation/Tutorials/Understanding%20the%20Planning%20Scene%20architecture
Basically, what you'll eventually want to do is generate a collision map from your kinect point cloud, and then publish a new planning scene containing the collision map to the environment server. After this, the collision map will be visible in the Planning Components Visualizer and Warehouse Viewer.
You will want to publish one of these messages:
http://www.ros.org/doc/electric/api/arm_navigation_msgs/html/msg/PlanningScene.html
And filling in the CollisionMap member of the message with one of these messages:
http://www.ros.org/doc/electric/api/arm_navigation_msgs/html/msg/CollisionMap.html
I believe that the pr2_arm_navigation_perception package has examples of how to do this.