Welcome Back to the Let's Encrypt Community, Doctor Christie 
Certbot-auto was just a wrapper around certbot, so nothing should really change in your process other than how you install and update certbot itself. You have been using the manual authenticator to satisfy dns-01 challenges to prove your ownership of the domain names. The standalone and webroot authenticators are used to satisfy http-01 challenges.
See @Osiris's post right below for an automated approach.
I can enhance your command a bit:
sudo certbot certonly --cert-name example.com --manual --preferred-challenges dns -d "example.com,*.example.com" --keep