I am confused and a wee bit lost here, please help....

In IH2 it says to "Merge" any files that maybe duplicated, understand merge no concern there. But do not know how/what to do on one it says to do it to. Before going further, I have installed it local only and it does appear to work even though I have not merged the below yet so I am lost as to IF I need to. ALL files are copied over to the store dir except this one.

tpl_main_page.php it is still in its default zip dir. I have this files duplicate in its custom folder now for cherry zen. No edits other than what cherry zen has in it.

The confusing is in IH2 tpl_main_page.php it has:

Code:
<?php
/**
 * Override Template for common/tpl_main_page.php
 *
 * @package templateSystem
 * @copyright Copyright 2005-2006 breakmyzencart.com
 * @copyright Portions Copyright 2003-2005 Zen Cart Development Team
 * @copyright Portions Copyright 2003 osCommerce
 * @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
 * @version $Id: tpl_main_page.php,v 1.1 2006/05/01 12:35:10 tim Exp $
 */
?>
<body id="popupAdditionalImage" class="centeredContent" onload="resize();">
<div>
<?php
// $products_values->fields['products_image']
  echo '<a href="javascript:window.close()">' . zen_image($_GET['products_image_large_additional'], $products_values->fields['products_name'] . ' ' . TEXT_CLOSE_WINDOW) . '</a>';
?>
</div>
</body>
In Cherry Zen (snipped for size) there is

Code:
  if (in_array($current_page_base,explode(",",'list_pages_to_skip_all_right_sideboxes_on_here,separated_by_commas,and_no_spaces')) ) {
    $flag_disable_right = true;
  }
  $header_template = 'tpl_header.php';
  $footer_template = 'tpl_footer.php';
  $left_column_file = 'column_left.php';
  $right_column_file = 'column_right.php';
  $body_id = ($this_is_home_page) ? 'indexHome' : str_replace('_', '', $_GET['main_page']);
?>
<body id="<?php echo $body_id . 'Body'; ?>"<?php if($zv_onload !='') echo ' onload="'.$zv_onload.'"'; ?>>
<?php
  if (SHOW_BANNERS_GROUP_SET1 != '' && $banner = zen_banner_exists('dynamic', SHOW_BANNERS_GROUP_SET1)) {
    if ($banner->RecordCount() > 0) {
?>
<div id="bannerOne" class="banners"><?php echo zen_display_banner('static', $banner); ?></div>
<?php
    }
  }
?>
Plus more below it. I do not know how/what I am suppose to merge as in my small pee brain tells me if I do I lose something from the cherry zen file, if I do not then I lose from IH2. Please advise what I am doing or rather thinking wrong here??/ Very Very little hair left....