The Pivot Points should be a lot easier to work with in version 5 than in version 4. You can adjust the Pivot Point from the Info section in the Object Controls Panel as well as the Effect Controls Panel in After Effects. If you are in the Invigorator Set-Up window, and adjust the Pivot Point Controls, be sure to click on the "Update Sets" button in the Effect Controls Panel when you get back into After Effects.
Hope this helps. If you're having problems setting the pivot point, please send me the project file and I can take a look at your setup. My e-mail address is email@example.com