I made a small change for an extra logo to the Bartik page.tpl.php file /themes/bartik/templates. This has the obvious disadvantage when upgrading say from 7.9 to 7.10 as it gets overwritten.

Is there a way to put a changed file somewhere else so that the change can get merged with future updates? http://drupal.org/node/190815 mentions copying it to your theme folder. Is this /sites/all/themes? I'm looking at the suggestions as well, and tried page_node.tpl.php in the /themes/bartik/templates folder, but that didn't work