Letsencrypt/configurationについて、ここに記述してください。

https://letsencrypt.readthedocs.org/en/latest/using.html#config-file

By default, the following locations are searched: 

    /etc/letsencrypt/cli.ini
    $XDG_CONFIG_HOME/letsencrypt/cli.ini (or ~/.config/letsencrypt/cli.ini if $XDG_CONFIG_HOME is not set).

# This is an example of the kind of things you can do in a configuration file.
# All flags used by the client can be configured here. Run Let's Encrypt with
# "--help" to learn more about the available options.

# Use a 4096 bit RSA key instead of 2048
rsa-key-size = 4096

# Always use the staging/testing server
server = https://acme-staging.api.letsencrypt.org/directory

# Uncomment and update to register with the specified e-mail address
# email = foo@example.com

# Uncomment to use a text interface instead of ncurses
# text = True

# Uncomment to use the standalone authenticator on port 443
# authenticator = standalone
# standalone-supported-challenges = tls-sni-01

# Uncomment to use the webroot authenticator. Replace webroot-path with the
# path to the public_html / webroot folder being served by your web server.
# authenticator = webroot
# webroot-path = /usr/share/nginx/html