First of all we still like CP but it has alot of bugs when you are going to use it with Enterprise.
First you gotta know that the config files are xml so CP does not really know how to work with them.
All the vhost conf are xml and imported as if it was apache. So now you setup you domain with a load of domain alliases and try to setup SSL for these domains.
Unfortunately, this doesnt work. All you going to achive is a ratelimit and you have to wait 2 days 
Cause of this nightmare is a wrong command line with “ACME.SH”
(DNS alias mode · acmesh-official/acme.sh Wiki · GitHub)
ALso for each you need create an extra TXT dns entry for each alias or you you can setup the dns api provided with acme.sh but dunno of this would even work with CP,
SOmewhere on this forum they advice you to create domain within your Main domain. Well sounds nice and also works but what if you only have a lincense for 5 domains and you have more aliassen. You will get a nice white screen that tells you that your over the domain limit and nothing will run.
Solution for this would be very easy:
- Install certbot
- null the acme entry in crontab
- remove the code block in you vhost entry that creates a context for /.wellknown …
- and mannually add everything
and never issue a ssl in CP it will probally fak up your ssl again
certbot will autorenew this for you.
CP should fix this asap, Why even use CP if you cannot even add aliasses with Enterprise.
command:
/usr/bin/certbot certonly --non-interactive --agree-tos --staple-ocsp -m [email protected] --no-eff-email --webroot -w /home/domain.nl/public_html -d domain.nl -d www.domain.nl -d alias.1.nl -d alias.2.nl -d alias.3.nl