For now, you need to go into appearance and click settings for the Commons Origins theme and then just save the setting form. Until we come up with a way to set the theme settings progmatically, this is what needs to be done.

- Main Menu
  - Home link gets class .main-menu-home (using module Menu Attributes - http://drupal.org/project/menu_attributes/)
  - Groups link gets class .main-menu-groups (using module Menu Attributes - http://drupal.org/project/menu_attributes/)
  - Events link gets class .main-menu-events (using module Menu Attributes - http://drupal.org/project/menu_attributes/)
  - Mennu is generated by menu_block and the block is assigned to the menu bar region

- Search
  - the search bar is assigned to the header region

- Adding a new pane
  If you want your new pane to have the white "pod" look as other areas of Commons, simply give it a class of .commons-pod in the pane creation/edit page and it will have the look consistant with the rest of the site.