Yeh its a bit tricky that one, have a look at the mail_menu.tpl, should be like this
<style type="text/css">
.left {
width: 150px;
float: left;
min-height: 300px;
padding: 5px 0 15px 5px;
}
.right {
float: left;
margin-left:10px;
padding-top: 5px;
}
</style>
<div class="left">
<?php if(isset($message)) {echo $message.'<br />';}
$folders = MailData::checkforfolders(Auth::$userinfo->pilotid);?>
<br />
<b>AIRPilot Mail Menu</b>
<ul>
<li><a href="<?php echo SITE_URL ?>/index.php/Mail/newmail">New message</a></li>
</ul>
<b>Folders</b>
<ul>
<li><a href="<?php echo SITE_URL ?>/index.php/Mail">AIRMail Inbox</a></li>
<?php
if (isset($folders)) {foreach ($folders as $folder) {echo '<li><a href="'.SITE_URL.'/index.php/Mail/getfolder?id='.$folder->id.'">'.$folder->folder_title.'</a></li>';}
}
?>
<li><a href="<?php echo SITE_URL ?>/index.php/Mail/sent">Sent Messages</a></li>
</ul>
<b>Folder Options</b>
<ul>
<li><a href="<?php echo SITE_URL ?>/index.php/Mail/newfolder">New Folder</a></li>
<li><a href="<?php echo SITE_URL ?>/index.php/Mail/deletefolder">Delete A Folder</a></li>
</ul>
</div>
And the mail inbox code should sit inbetween the <div class="mcright"> divs.
Give that a try.