Hello 
I'm assuming you're using GoDaddy cPanel shared hosting. You want a separate certificate for each apex (primary) domain name that covers its alias subdomain names. For example.com, I recommend a certificate covering example.com, www.example.com, and mail.example.com. I authored the CertSage ACME client specifically to help GoDaddy shared hosting users easily acquire Let's Encrypt certificates. With cPanel, your primary domain name's webroot directory is usually public_html and your secondary domain names' webroot directories are under public_html like public_html/whatever.com. You would put a copy of certsage.php in public_html and in each of your secondary domain names' webroot directories with those secondary certsage.php copies having line 18 modified from this:
public $dataDirectory = "../CertSage";
to this:
public $dataDirectory = "../../CertSage";