You can manually renew expiring certificates in the Dashboard → System & Settings → HTTPS → HTTPS certificates page of your concrete5 installation (next you'll need to tell Apache/nginx to reload the new HTTPS certificate files).
By the way, for security reasons the Let's Encrypt certificates have a short validity (90 days at the time of writing this), so this could become tedious.
You can automate the certificate renewals by scheduling a shell script to be run on your webserver.
Indeed, this package comes with the command le:renew command that can be used in a terminal instance.
For example, here's how you can schedule certificate renewal if your web server have Apache and Ubuntu:
/path/to/webroot/concrete/bin/concrete5 le:renew && service apache reload