If you want to use the box inthebox as Regions in PHPTemplate
make a file template.php and write in there

function inthebox_regions() {
  return array(
    'left'  => t('left sidebar'),
    'right' => t('right sidebar'),
    'content' => t('content'),
    'header' => t('header'),
    'footer' => t('footer'),
    'box' => t('box')
    
  );
}
?>

Then open page.tmp.php
and modified the code

				<div class="sidebar" id="main-content-right">
          				<div id="square-ads"><img src="themes/inthebox/passat_square.gif" alt="ads" /></div>
									<?php if ($sidebar_left != ""): ?><div class="sidebar" id="sidebar-left"><?php print $sidebar_left ?></div><?php endif; ?>				                  <?php if ($sidebar_right != ""): ?>
                  <div class="sidebar" id="sidebar-right"><?php print $sidebar_right ?></div><?php endif; ?>
				</div>
 <br class="clear" />  

to ---->

				<div class="sidebar" id="main-content-right">
						<?php if ($box != ""): ?>
          				<div id="box">							
						<?php print $box ?>					
				        </div>
						<?php endif; ?>
				
									<?php if ($sidebar_left != ""): ?><div class="sidebar" id="sidebar-left"><?php print $sidebar_left ?></div><?php endif; ?>				                  <?php if ($sidebar_right != ""): ?>
                  <div class="sidebar" id="sidebar-right"><?php print $sidebar_right ?></div><?php endif; ?>
				</div>
 <br class="clear" />

The go to admin>block and make a block for the box
That’s it