You would put a copy of certsage.php into the webroot directories of:
websiteone.org
websitetwo.org
websitethree.org
then acquire and install three certificates, one at a time, where each certificate covers a website.org and www.website.org.
The three webroot directories would be something like:
public_html
public_html/websitetwo.org
public_html/websitethree.org
Keep in mind that CertSage is entirely operated from the webpage presented to you when you visit http://website.org/certsage.php.
The full instructions can be found here: