So I added the path /usr/local/src/letsencrypt/letsencrypt-auto for my lets encrypt client command in Webmin configuration. I was then able to use the Let’s Encrypt menu tab for Managing SSL Certificate for each of my virtual domains by just clicking Request Certificate. Are you going to add an option within the Let’s Encrypt menu to add a schedule to renew the certificates?
The current automatic renewal script has some serious issues. I’d suggest to just use letsencrypt renew and link to the certs in the /etc/letsencrypt/live/hostname.domain.tld directory. It’s very easy to set up. Then essentially just call it every now and then (cron-script for example) and it’ll figure out whether or not any certificates in /etc/letsencrypt need renewal (aka expires in the next 30 days or so). More info here.