I keep seeing about how the script will automatically create the certificate. Will I be able to also do this manually?
The closest I’ve seen to this is (from https://letsencrypt.org/howitworks/)
Without Automatic Web Server Configuration
$ letsencrypt -d example.com auth
The official client has a “manual” mode, and other clients can, of course, implement different manual modes that may prove more suitable for your use case.
For example, Boulder has a (not secret) Node.JS ACME client inside its repo that is just about as manual as using
curl. It’s certainly not intended as a user friendly product, but we use it for integration testing, so it works.