I highly recommend the following way for changing header and footer. Default header and footer is located at

design/defaulttheme/tpl/pagelayouts/parts/page_head_logo.tpl.php
design/defaulttheme/tpl/pagelayouts/parts/page_footer_user.tpl.php

In order to change header or logo just copy templates from defaulttheme to customtheme

design/customtheme/tpl/pagelayouts/parts/page_head_logo.tpl.php
design/customtheme/tpl/pagelayouts/parts/page_footer_user.tpl.php​

That way you will override default header and footer content without changing default designs.

We also have a dedicated extension related to these types of changes please refer to this article.