I’m not aware of a good cpanel tutorial for Let’s Encrypt - although there may be one.
On cpanel servers where you have root access ( it looks as if you have a VPS with root access from what you say) I use a relatively simple method of automation ( that works fine for me ) .
Check the current location where cpanel has stored your SSL certs. I’m assuming you are probably on CentOS - so check the file /etc/httpd/conf/httpd.conf for SSLCertificateFile for your domain the lines there will be something like
The numbers will be all different - but there should be the locations for the domain certificate, private key and CA cert
In the cron, that renews your Let’s Encrypt certificates, simply update those locations. You could change those locations for symlinks to the /etc/letsencrypt/live/iguanathemes.com files.
That way, you don’t need to paste manually into the GUI, it all simply happens automatically every couple of months.