Custom Post Type Pagination & duplicate posts

I’m working on a template which will use some custom-post-types & custom-taxonomies.. I’m having problems with pagination and duplicate posts.

HOME.PHP

LOOP #1
On the homepage (home.php) I have 2 Loops. The fist one shows 1 post (custom post type: Projects) which has the custom-taxonomy “Featured” assigned to it.

LOOP #2
On the second loop I have the six most recent “Projects” (Custom post type) but I dont want a duplicate from the first loop. Under the six posts I’d like a pagination

Both loops in home.php work.. but I still have that duplicate and I can’t get pagination to work..

PasteBin

• home.php: http://pastebin.com/6ac2asue

• functions.php: http://pastebin.com/1SK206Bh

  <?php $do_not_duplicate = array();
  $folio_loop = new WP_Query( array
      (
          'featured' => 'featured-post',
          'post_type' => 'projects',
          'posts_per_page' => '1',
          )
      );
  
       while ( $folio_loop->have_posts() ) : $folio_loop->the_post();
      $do_not_duplicate[] = $post->ID; ?>
  
      <div id="featured" style="position: relative;">
  
  
          <div class="featured-overlay" style="position: absolute; right: 20px; bottom: 20px; width: 165px; height: 165px; text-align: center;">
              <div class="project-meta-featured">
            <a href="https://wordpress.stackexchange.com/questions/69853/<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>" >
          <span>
          <?php
              global $post;
              $text = get_post_meta( $post->ID, '_cmb_project_meta', true );
              echo $text;
          ?>
          </span>
          <br />
          <?php
              global $post;
              $text = get_post_meta( $post->ID, '_cmb_client_meta', true );
              echo $text;
          ?>
  
  
          </a>
            </div>
          </div>
  
          <?php if ( has_post_thumbnail()) : ?>
              <a href="https://wordpress.stackexchange.com/questions/69853/<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>" >
                  <?php the_post_thumbnail('featured'); ?>
              </a>
          <?php endif; ?>
  
  
  
      </div>
  
  <?php endwhile; ?>
  

I think the best way to implement this is to use pre_get_posts hook. Take a look at this code

function customize_query( $query ) {
    $post = get_posts(array(
         'post_type' => 'projects',
         'taxonomy' => 'featured',
         'numberposts' => 1
    ));
    if ( $query->is_home() && $query->is_main_query() ) {
        $query->set( 'post_type', 'projects' );
        $query->set( 'posts_per_page', 6 );
        if($post && !empty($post))
            $query->set( 'post__not_in', array($post[0]->ID) );
    }
}
add_action( 'pre_get_posts', 'customize_query' );

Then in your home page

$post = get_posts(array(
     'post_type' => 'projects',
     'taxonomy' => 'featured',
     'numberposts' => 1
));
// display the post just retrieved, it must be coming from cache

// we can use the global query since now it contains the 6 posts we want
while(have_posts()) :
    the_post();
    // display the post
endwhile;

You’ll need to modify it a lot but it might help you achieve what you want. In here the pagination should wotrk as normal since you just modified the main page query