Do not use Certbot on cPanel. It is not compatible. Apache configuration is distilled by cPanel in a very specific way. If Certbot modifies the configuration, it will fuck everything up. Same deal with Engintron.
Just use AutoSSL as it was intended.
There's no direct equivalent. You can find all of the state here:
/var/cpanel/ssl
and also
/home/$USER/ssl/{certs,keys}
But you should not rely on the existence or structure of that directory. Use the WHM API if you need to retrieve data about certificates.
An exception could be if the specific subdomains aren’t administered with cPanel at all. In that case you could choose to use Certbot for those domains but not for the others (especially if they’re not mentioned in the Apache configuration but exclusively in the configuration of the other servers).
However, I would definitely agree that you’ll have a better and more reliable experience if you find a way to use the same administration method for all of your subdomains, which is generally by following @_az’s advice.