For example, your Site is reachable under www.example.com under the directory /var/www/
and your WordPress-Blog is under /var/www/newsite/
, than put the robots.txt in /var/www/
and change the folders in there:
Disallow: /newsite/wp-admin/
Disallow: /newsite/wp-includes/
Disallow: /newsite/wp-content/plugins/
Why /newsite/wp-admin/
and not /var/www/newsite/wp-admin/
for example?
The directory is relative from the URI like http://www.example.com/newsite/