http://wordpress.org/support/topic/need-help-modifying-loop-

<?php
// Template Name: HomePage
/**
 *
 * @package progression
 * @since progression 1.0
 */

get_header(); ?>
<?php get_sidebar(); ?>

<section id="content">

    <!-- this code pull in the homepage content -->

    <?php while(have_posts()): the_post(); ?>

        <?php $cc = get_the_title(); if($cc != '') { ?>
        <h1 class="page-title"><?php the_title(); ?></h1>
        <?php } ?>

        <?php $cc = get_the_content(); if($cc != '') { ?>
            <div id="home-page-content">
                <?php the_content(); ?>
            </div>
        <?php } ?>

    <?php endwhile; ?>



    <?php
    global $more;    // Declare global $more (before the loop).
    ?>
    <div id="mason-layout" class="transitions-enabled fluid">
    <?php
    if ( get_query_var('paged') ) {
        $paged = get_query_var('paged');
    } else if ( get_query_var('page') ) {
        $paged = get_query_var('page');
    } else {
        $paged = 1;
    }


    $postIds = get_post_meta($post->ID, 'pageoptions_blog_category', true); // get custom field value
        $arrayIds = explode(',', $postIds); // explode value into an array of ids
        if(count($arrayIds) <= 1) // if array contains one element or less, there's spaces after comma's, or you only entered one id
        {
            if( strpos($arrayIds[0], ',') !== false )// if the first array value has commas, there were spaces after ids entered
            {
                $arrayIds = array(); // reset array
                $arrayIds = explode(', ', $postIds); // explode ids with space after comma's
            }

        }

    $postspage = get_post_meta($post->ID, 'pageoptions_pstsperpage', true);

    query_posts( array( 'posts_per_page'=> $postspage, 'paged' => $paged, 'tax_query' => array(
        array('taxonomy' => 'category',
                            'terms' => $arrayIds,
                            'field' => 'slug'
       ))
     ) );

    $count = 0;                     // Set counter to 0 outside the loop
    // begin the loop
    if (have_posts()) : while (have_posts()) : the_post();

        /* Set up and display Post Archive */
        $more = 0;              // Set to display content above more
        get_template_part('content','blog');    // Get content
        $count++;               // Increment counter by 1

        /* Set up and display AdRotate content */
        if ($count % 5 == 0){           // Returns True every 5th post
            echo '<div class="ad">';
            adrotate_group(1);      // Displays Ads on Frontend
            echo '</div> <!-- /.ad -->';
        }
    endwhile;
?>
    <div class="clearfix"></div>
    </div><!-- close #mason-layout -->


    <?php get_template_part( 'pagination', 'blog' ); ?>



<?php elseif ( current_user_can( 'edit_posts' ) ) : ?>
    <?php get_template_part( 'no-results', 'index' ); ?>
    <?php endif; ?>

<?php get_footer(); ?>