Thanks for your comment, this would be the fall back solution for sure but I think the future of WP theming is using filters and hooks to modify the parent theme without having to resort to your own index.php header.php etc. This is just a much cleaner and forward thinking way of developing so that upgrading WP doesn’t break your theme..
So any php gurus out there that can help? Thematic theme has a lot more support for people using filters and hooks only it seems so I may switch to that theme as my parent..