Removing duplicate values between two wordpress queries

Question

I'm addressing a well known issue in Wordpress, in which I want to display "featured" posts, and under it the rest of the posts.
I have a $query1 which holds 2 featured posts, and my query_posts which holds all of the posts on the site (including those two from $query1).
I now wish to remove from query_posts those two posts so I can display it using regular Wordpress loop in the form of:

while (have_posts ()) : the_post();
the_title();
the_content();
endwhile;

I have the solution for removing these duplicate posts inside the above loop, but because of the paging, I want to have the query without duplicates before that, so the query_posts array will be paged without those two featured posts.

Answer 1

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.