Instead of moving the "New Products" above the main content (in define_main_page.php), you could move the main content to after the new products. If you don't already have the file tpl_index_default.php in the directory /includes/templates/classic/templates, then copy the file from /includes/templates/template_default/templates and then edit as described below.
P.S. You should really have your own, custom template instead of using the 'classic'. Keeping the classic template pure allows you to switch between templates see if issues you're having are template-specific or site-wide.
Code:
<?php if (DEFINE_MAIN_PAGE_STATUS >= 1 and DEFINE_MAIN_PAGE_STATUS <= 2) { ?>
<?php
/**
* get the Define Main Page Text
*/
/*
?>
<div id="indexDefaultMainContent" class="content"><?php require($define_page); ?></div>
<?php */ } ?>
<?php
$show_display_category = $db->Execute(SQL_SHOW_PRODUCT_INFO_MAIN);
while (!$show_display_category->EOF) {
?>
<?php if ($show_display_category->fields['configuration_key'] == 'SHOW_PRODUCT_INFO_MAIN_FEATURED_PRODUCTS') { ?>
<?php
/**
* display the Featured Products Center Box
*/
?>
<?php require($template->get_template_dir('tpl_modules_featured_products.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_featured_products.php'); ?>
<?php } ?>
<?php if ($show_display_category->fields['configuration_key'] == 'SHOW_PRODUCT_INFO_MAIN_SPECIALS_PRODUCTS') { ?>
<?php
/**
* display the Special Products Center Box
*/
?>
<?php require($template->get_template_dir('tpl_modules_specials_default.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_specials_default.php'); ?>
<?php } ?>
<?php if ($show_display_category->fields['configuration_key'] == 'SHOW_PRODUCT_INFO_MAIN_NEW_PRODUCTS') { ?>
<?php
/**
* display the New Products Center Box
*/
?>
<?php require($template->get_template_dir('tpl_modules_whats_new.php',DIR_WS_TEMPLATE, $current_page_base,'templates'). '/tpl_modules_whats_new.php'); ?>
<?php if (DEFINE_MAIN_PAGE_STATUS >= 1 and DEFINE_MAIN_PAGE_STATUS <= 2) { ?>
<?php
/**
* get the Define Main Page Text
*/
?>
<div id="indexDefaultMainContent" class="content"><?php require($define_page); ?></div>
<?php } ?>
<?php } ?>
<?php if ($show_display_category->fields['configuration_key'] == 'SHOW_PRODUCT_INFO_MAIN_UPCOMING') { ?>
<?php
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