Thank you for providing the way to beat the GoDaddy SSL prices. I successfully installed CertSage.php and it worked on my main domain. I have a subdomain leading to one of the folders within the same hosting. I followed your instructions to the dot, but it does not work for the second domain. I opened www.main.com/certsage.php without any problems. For the second one I open main.com/second/certsage.php, to get SSL for the second.com. Second.com resides at the main.com/second/index.html, so it is impossible to visit second.com/certsage.php, it doesn't exist. What can I do to make sure Second.com domain is accessible and safely leads to main.com/second?
Please open your own new thread instead of hijacking someone elses, thank you.
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Welcome to the Let's Encrypt Community! 
You need to be able to visit http://second.com from the internet in order to use CertSage to acquire a certificate for second.com. The URL https://main.com/second/index.html is already covered by the certificate for main.com. That's not a URL under second.com. I think you might be confusing how addon domain names work cPanel. Yes, their content lives in a directory inside the directory for the main domain name. However, you're not supposed to access that content using the main domain name. This guide describes in detail how to setup CertSage for addon domain names:
Without knowing your actual domain names, it is very difficult to help you properly. I suspect that you have some type of redirection in place, which makes things a bit more complex.
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