WP_Query_Multisite is a subclass of WP_Query, WordPress' post querying class. The class does everything behind the scenes, so the only change you make to query multisite is the in the class declaration expression. 

Example usage:

$query = new WP_Query_Multisite( array('post_type' => 'post' ) );
while($query->have_posts()) : $query->the_post();
    echo $blog_id . get_the_title() . "<BR>";
endwhile; 
wp_reset_postdata();

To modify what sites are queried, create a 'sites' element in the $args in the constructor parameter, with a sub-element of either 'sites__in' or 'sites__not_in', which will be an array similar to 'posts__in' in the WP_Query object. 

EX: 

$args = array(
	'post_type' => 'post',
	'sites' => array(
		'sites__in' => array( 1, 2, 3, 5)
	)
);
$query = new WP_Query_Multisite( $args );
while($query->have_posts()) : $query->the_post();
    echo $blog_id . get_the_title() . "<BR>";
endwhile; 
wp_reset_postdata();