Since the header.php and footer.php files are pure PHP and not parsed by Unicity CMS, if you wish to use merge tags within these files, you will need to access the PHP variables instead of using the standard merge tags.
If you have an editable region with the merge tag MainIntroText, you are probably used to using this in your .tmpl files using the merge tag %contentMainIntroText%
.
In header and footer files you instead need to access the PHP variable, $contentMainIntroText
.
Remember that these PHP variables contain the raw content stored in them, and are not parsed by Unicity CMS. If the content you are including in your template may contain module codes, you would need to process these first, allowing modules to be embedded within these areas of content. This uses the core processModules function, for example:
print( processModules( $contentMainIntroText ) );