First of all I would like to thanks for project of let's encrypt. I was using comodo ssl last 5 days I had I decided to change with lt's encrypt. To setup ssl I use webmin/wirtualmin as it is setup in my VPS server (ubuntu 15 64 bit).
On Webmin panel I can see private key file (/etc/webmin/letsencrypt-key.pem) and also certificate file (/etc/webmin/letsencrypt-cert.pem) also additional certificate files (/etc/webmin/letsencrypt-ca.pem).
Everyting is look okay but when I open my website on mozilla firefox still I can see "verified by comodo ca.