How to update serialized post meta?

You must read custom field themeOps first, update index option3 in array and then save/update whole array.

$kisiArray = get_post_meta( $post_id, 'themeOps' );
$kisiArray['option3'] = 'peach';
update_post_meta( $post_id, 'themeOps', $kisiArray );

Update (sort by custom field)

$args = array(
    'post_type'  => 'post',
    'meta_key'   => 'themeOps_option3',
    'orderby'    => 'meta_value_num',
    'order'      => 'ASC',
);
$query = new WP_Query( $args );

More examples you find in Codex