The file /etc/php5/cgi/php.ini is correct if you have not set any custom php.ini entrys in ispconfig. Dont forget to restart apache after you changed the file. In case that you had set values in the custom php.ini field in the website settings in ispconfig, then this site has its own php.ini and all changes should be done in the custom php.ini field then, the get merged into the correct php.ini filefor the site automatically.
