<div class="metabox-prefs">
    <?php
        meta_box_prefs( $this ); // draw checkboxes in screen options
    ?>
</div>

function meta_box_prefs( $screen ) {
    global $wp_meta_boxes;

    $hidden = get_hidden_meta_boxes($screen);

    // hide some boxes
}

function get_hidden_meta_boxes( $screen ) {
    // code
    $hidden = apply_filters( 'default_hidden_meta_boxes', $hidden, $screen );
    // code
    return apply_filters( 'hidden_meta_boxes', $hidden, $screen, $use_defaults );
}