Removing duplicate values between two wordpress queries

Based on several different answers, with a SPECIAL thanks to EAMann‘s similar answer – here’s the method I followed.

1. Using new WP_Query instead of query_posts for this page.
2. Defining the query variable ($main_query) as global.
3. Querying a temp array ($temp_featured) with my featured posts.
4. Creating an array with only the IDs of the `$temp_featured’. Note EAMann’s use of the wp_list_pluck function.
5. Executing the main query of the page ($main_query) with the argument to exclude the IDs retrieved in #4.

This is how it came out all in all:

global $main_query; 

$temp_featured = get_posts( 
    array(
        'post_type' => 'custom_post',
        'custom_post-category' => 'featured-cat', 
        'posts_per_page' => 2)
        );
$featured_ids = wp_list_pluck( $temp_featured, 'ID' );

$query_args =  array(
                'post_type' => 'custom_post',  
                'posts_per_page' => $per_page, 
                'paged' => $current_page, 
                'post__not_in'   => $featured_ids
                );
$main_query = new WP_query ($query_args);

//displaying the two featured posts with their own query
$featured = new WP_query( array(
                            'post_type' => 'custom_post',
                            'custom_post-category' => 'featured-cat',
                            'posts_per_page' => 2)
                            );
while ($featured->have_posts ()) : $featured->the_post();
    the_title();
    the_excerpt();
endwhile;

//displaying the full query of the page
if ($main_query->have_posts ()) : 
    while ($main_query->have_posts ()) : $main_query->the_post();
        the_title();
        the_excerpt();
    endwhile;
endif;

I hope this helps anyone – please edit/comment or contact me if you have some further thoughts or inquiries.