Let's Encrypt and proxy site

I'd do the following.

First, install your Ghost and take note of the port it is configured to listen. Let's assume it is 2368 from now on.

Second you create an HTML site with Let's Encrypt. Don't forget you need domain.com and www.domain.com pointing to your server.

ee site create example.com --le

Now modify the vhost configuration file to add support to the Ghost backend.

ee site edit example.com

Add the @ghost handler to it (or any other name you wish, as long as it does not conflict with any other configuration):