Drupal gives `Notice: Undefined index: highlighted in include ..` error during theme creation
this is probably stemming from the default page.tpl.php which is expecting to find a region highlighted.  The best approach IMHO would be to create a custom page tpl that excludes the regions you don't use, and includes the regions you do.

You can find the default page.tpl.php under modules/system - just copy the file to your theme directory (or sub folder templates) make the changes you want, and then clear the cache