We run a number of WordPress Multisite installations on our dedicated server for a variety of clients.  Our largest installation, for Share the Practice, currently consists of 88 individual WordPress sites.  A number of these sites use sub-domains, but for most of them we map custom domain URLs onto the main WordPress Multisite installation.

WHM / cPanel now offers easy SSL installation, but there is a small catch: it only allows 200 domains per virtual host, and the documentation about this is a little confusing.  We had been using the “Park” or “Alias” function in cPanel to handle the mapping for each domain, but then ran over the limit, as WHM creates multiple subdomains for each domain you add that way.

The workaround for this was to use “Addon Domain” instead of “Alias”.  This creates a separate virtual host for each domain, and will therefore enable an individual SSL certificate for each, getting around the 200 domain limit.

WARNING:
Before you make any of these changes, make sure to check for any setup email accounts, email forwarders, or any custom DNS settings (subdomains, custom MX records, CNAME records, etc).  These will all be deleted without warning if you proceed, so make sure you have backups before you do any of this.  If you do have custom DNS settings, copy them down and then re-add once you’ve switched the domain(s).

To make this work, we followed these steps:

1. Sign into your cPanel account
2. Open up Aliases
3. Check that a given domain does NOT have email accounts or email forwarders set.
4. If NO email forwarders or accounts have been set up, first copy the domain name, then click the “Remove” link for the domain on the Aliases page.
5. Create a new Addon Domain (paste the domain name into the field).  For a WordPress Multisite installation, set the Document Root to be public_html (or wherever your installation lives in the parent account).
6. Repeat for each domain you want to switch over, until you get back below the 200 domain limit.
7. AutoSSL will attempt to regenerate your SSL certs each time you add a new Addon Domain.
8. Review the AutoSSL logs in WHM to check for any errors in the SSL certificate creation process

Hope this helps!