Dear tphmedia,
In order to add a module to the header section, please open templatesja_portfolioblocksheader.php and edit as follow:
change lines 31
<?php if($this->countModules('search')) : ?>
<div id="ja-search">
<jdoc:include type="modules" name="search" />
</div>
<?php endif; ?>
to
<?php if($this->countModules('yournewmodule')) : ?>
<div id="ja-yournewmodule">
<jdoc:include type="modules" name="yournewmodule" />
</div>
<?php endif; ?>
<?php if($this->countModules('search')) : ?>
<div id="ja-search">
<jdoc:include type="modules" name="search" />
</div>
<?php endif; ?>
and please style for it.