You want Posts 2 Posts which allows you to create many to many (or one to many or many to one) relationships between post objects — including custom post types.
To related stores and deals you might do something like this…
<?php
add_action('p2p_init', 'wpse102461_connection');
function wpse102461_connection()
{
p2p_register_connection_type(array(
'name' => 'stores_to_deals',
'from' => 'STORES', // or whatever your custom post type actual is
'to' => 'DEALS', // or whatever your deals type is
));
}
This will create the admin interface (which you can customize) for you and provide a way to fetch associated deals.
Or you could overload post_parent
to do what you need.