setting up letsencrypt certificates for multiple virtual hosts with apache

The preferred method is to just run certbot multiple times with each required domain, as mentioned at https://www.digitalocean.com/community/tutorials/how-to-set-up-let-s-encrypt-certificates-for-multiple-apache-virtual-hosts-on-ubuntu-14-04 

So, sudo certbot --apache -d example.com -d www.example.com

and later

sudo certbot --apache -d example2.com -d www.example2.com

or whatever. And then add to root's cron,

15 3 * * * /usr/bin/certbot renew --quiet

which checks every morning at 3:15 AM and renews any certs with validity less than 30 days more.