I'm getting a 404 for http://juanita.org.uk/certsage.php and you should NEVER have password.txt (or a CertSage data directory or any of its contents) in your public_html folder (or ANY of its subfolders). Anything in public_html is accessible from the internet. Having confidential information located there creates a significant security risk. If you are attempting to use CertSage with multiple domain names hosted under one cPanel account, there are extra steps you need to take to configure things correctly, but it can be done (griffin.software and certsage.com are configured this way).
cPanel hosts the first/primary/main domain name directly in /public_html and subsequent/secondary/add-on domain names in subfolders inside /public_html. There is a subdomain of the primary domain name associated with each of these secondary domain names. For example, primary.com would have its webroot as /public_html and be accessible via http://primary.com while secondary.com would have its webroot as /public_html/secondary.com and be accessible via http://secondary.com and http://secondary.com.primary.com (no, I'm not kidding; try it). For primary.com, CertSage can be used in the simplest, standard way. If you want to be clever, you could modify line 18 of that certsage.php from "../CertSage" to "../CertSage.primary.com" just to make it very clear which domain name that CertSage folder belongs to. For secondary.com, there are a few more steps.
When you put a copy of certsage.php in /public_html/secondary.com, you should modify line 18 of its certsage.php to have "../../CertSage.secondary.com" instead of just "../CertSage". This will create a unique data directory (and password.txt file and Let's Encrypt ACME account) for secondary.com. Each ACME account has its own set of email addresses for receiving expiration notices, so you'll need to register those individually for each domain name. You can modify any password.txt file to contain whatever you want to use for your CertSage password. You can make them all the same if you wish. You need to add an A record to your DNS for primary.com (at the real DNS provider, not inside cPanel) that points a subdomain named secondary.com to the same IP address as the A record for primary.com (usually denoted with an @ symbol as the subdomain name).
When you request a certificate for secondary.com using CertSage, you should specify secondary.com, mail.secondary.com, and secondary.com.primary.com (and www.secondary.com if you use it) as the domain names in the box for which you wish to acquire a certificate. You can install that certificate into cPanel using the button in CertSage per usual. However, to force HTTP to HTTPS redirection for secondary.com, you need to log into your cPanel (https://primary.com:2083/). Go to the Domains section in cPanel and click on the Domains tool in that section. Expand the section for secondary.com.primary.com and toggle Force HTTPS Redirect to "on".