Today I do the following:
/usr/bin/letsencrypt renew -n --agree-tos --email [email protected] --keep-until-expiring
Will I need to change that? Will I need to manually add custom DNS entries to all my domains?
PS To add, compared to dealing with some paid certificate services, LetsEncrypt has been a dream.
This adds a new validation method that people can use if they want. The existing validation methods (https://letsencrypt.org/docs/challenge-types/) aren't going away, so your current setup will keep working.