How can I loop into two different DIVS without repeating the DIVs

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The key, I think, to what you are doing is to use “offset”

<div class="col4 inner-left">
    <ul class="popular-list">
        <?php
        query_posts('order=DESC&posts_per_page=3&post_type=pop');
        if (have_posts()) : while (have_posts()) : the_post(); ?>
            <li>
                <a href="https://wordpress.stackexchange.com/questions/125200/<?php the_permalink(); ?>"><?php the_title(); ?></a>
            </li>
        <?php endwhile; endif; ?>          
    </ul>
</div>
<div class="col4 inner-right">
    <ul class="popular-list">
        <?php
        query_posts('order=DESC&posts_per_page=3&post_type=pop&offset=3');
        if (have_posts()) : while (have_posts()) : the_post(); ?>
            <li>
                <a href="https://wordpress.stackexchange.com/questions/125200/<?php the_permalink(); ?>"><?php the_title(); ?></a>
            </li>
        <?php endwhile; endif; ?>          
    </ul>
</div>

<?php // Reset Query
wp_reset_query(); ?>

http://codex.wordpress.org/Class_Reference/WP_Query#Pagination_Parameters

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