Well, there are two methods, depending how technical you are.
You could get the certificates ( from /etc/letsencrypt/live/domain ) and paste them into cpanel. This is the way you would almost have to do it the very first time, but is a manual method, so can’t easily be automated.
Check in your /etc/httpd/conf/httpd.conf file for where it is referencing the current certificates.
You can do a simple check with
grep SSLCertificate /etc/httpd/conf/httpd.conf
although this will show you all of them, and not where they are easily for each domain. You can edit the file though ( or use “less /etc/httpd/conf/httpd.conf” to view it) and find where they are.
For domains they are likely to be at some location like;
If you copy that current certificate (as a backup), delete it, and create a symlink to the correct certificate
ln -s /etc/letsencrypt/live/domain/cert.pem /var/cpanel/ssl/installed/certs/domainname_com_b76a5_a7466_1463960_00f1df1b93e67ad82d24eaf55105600e.crt
Then it will create a symlink to the correct files ( which will be updated by letsencrypt ) so renewing in the future you simply need to run the letsencrtpy / certbot to get a new cert, and then restart apache to use it. Hence it can be automated.