Digital Ocean has a pretty good guide for setting up Lets Encrypt with Nginx on Ubuntu 14.04. However, their guide requires you to turn down your Nginx server while initially getting you Lets Encrypt TLS certificates, this of course is problematic for server/site operators who either need or want to continue to have service continuity while getting lets Encrypt Certificates. They also don’t explain how to use subject alternative names to handle multiple sub domains on the same server.
Lets Encrypt’s software requires that they be able to connect to your server to verify that the domain you’re attempting to register a certificate for you control. In the Digital Ocean guide, this process is handled by using the built-in web server in the lens encrypt package. However, Lets Encrypt does not need to operate in this manner to create new certificates, it can use the wwwroot/filesystem approach and your existing server configuration.
The process is very similar to Digital Oceans guide, but the order of operations are slightly different.