Without a proper SQL query in the question is not possible to write a proper query in the response, but following your pseudo-code approach:
SELECT custom-data
FROM custom-table
LEFT JOIN wp_users ON custom_data.user_id = wp_users.ID
LEFT JOIN wp_usermeta ON wp_users.ID = wp_usermeta.user_id
WHERE some-condition
AND wp_usermeta.meta_key = 'flag'
AND wp_usermeta.meta_value="flagvalue"
So basically, you need to join against wp_usermeta, which is where you’d be storing your users “flag”.