To manually copy your certificates to dovecot and postfix so that your mail clients do not display a warning about bad certificates follow these steps.
You will want to copy the latest certificate which will be located in the folder name starting with your primary domain followed by largest the iteration number.
Copy your private keys
cp /etc/letsencrypt/archive/server1.domain.ca-0005/privkey1.pem /etc/dovecot/private/dovecot.pem
cp /etc/letsencrypt/archive/server1.domain.ca-0005/privkey1.pem /etc/postfix/postfix.key.pem
Copy your certificates
cp /etc/letsencrypt/archive/server1.domain.ca-0005/cert1.pem /etc/dovecot/dovecot.pem
cp /etc/letsencrypt/archive/server1.domain.ca-0005/cert1.pem /etc/postfix/postfix.cert.pem
Copy your fullchain
cp /etc/letsencrypt/archive/server1.domain.ca-0005/fullchain1.pem /etc/dovecot/dovecot.ca.pem
cp /etc/letsencrypt/archive/server1.domain.ca-0005/fullchain1.pem /etc/postfix/postfix.ca.pem
Restart the Services
service dovecot restart
service postfix restart