How do you create a custom Panels layout in an Omega sub-theme?
The basic process is:

Edit the MYTHEME.info file:

; PLUGINS
plugins[panels][layouts] = panels/layouts


Create a directory in panels/layouts/mypanel

Create your include panels/layouts/mypanel/mypanel.inc

/**
 * Implements hook_panels_layouts().
 */
function mytheme_mypanel_panels_layouts() {
  $items['mypanel'] = array(
    'title' =&gt; t('My Panel'),
    'category' =&gt; t('My Site'),
    'icon' =&gt; 'mypanel.png',
    'theme' =&gt; 'mypanel',
    'regions' =&gt; array(
      'top' =&gt; t('Top'),
      'left' =&gt; t('Left column'),
      'right' =&gt; t('Right column')
    ),
  );

  return $items;
}


Create your 50x75 mypanel.png, and place it as panels/layouts/mypanel/mypanel.png

Create the template file as panels/layouts/mypanel/mypanel.tpl.php

&lt;div class="panel-display mypanel" &lt;?php if (!empty($css_id)) { print "id=\"$css_id\""; } ?&gt;&gt;
    &lt;div class="panel-panel mypanel-top grid-16 alpha omega"&gt;
        &lt;div class="inside"&gt;&lt;?php print $content['top']; ?&gt;&lt;/div&gt;
    &lt;/div&gt;

    &lt;div class="panel-panel mypanel-left prefix-1 grid-4 alpha"&gt;
        &lt;div class="inside"&gt;&lt;?php print $content['left']; ?&gt;&lt;/div&gt;
    &lt;/div&gt;

    &lt;div class="panel-panel mypanel-right grid-9 suffix-1 omega"&gt;
        &lt;div class="inside"&gt;&lt;?php print $content['right']; ?&gt;&lt;/div&gt;
    &lt;/div&gt;
&lt;/div&gt;


Upload, clear cache, and see if you can make a panel page.  Nine times out of ten, the problem with Panels picking up custom panel layouts has to do with a misnamed include or template file, which I suspect is your problem.