You can configure your custom region in the theme / config.php file, for example -
'course' => array( 'file' => 'general_layout.php', 'regions' => array('side-pre', 'bottom-region' ), 'defaultregion' => 'side-pre', 'options' => array('langmenu' => true), ),
And define the area in the theme layout file /layout/yourlayout.php
<div id="region-pre" class="block-region"> <div class="region-content"> <?php echo $OUTPUT->blocks_for_region('bottom-region') ?> </div> </div>
See moodle doc for details - http://docs.moodle.org/dev/Themes_2.0
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