Using VHOST and express it is possible to host multiple websites using a single server.
The included files cover the general idea to get you up and running.
(Running Ubuntu 14.04 LTS) When using Let's encrypt, you will do the following commands:
Add Certbot to your list of software available
sudo add-apt-repository ppa:certbot/certbot
Update all software references
sudo apt-get update
Install Certbot
sudo apt-get install certbot
Create Certificates for your different domains
certbot certonly --standalone -d siteOneDomain.com -d www.siteOneDomain.com -d siteTwoDomain.com -d www.sitetwoDomain.com
Update siteOneDomain and siteTwoDomain to your own domains and add as many sites will multi-use this certificate by adding -d newsitename.com -d www.newsitename.com.
So make sure you include both with and without www.
When it has been completed it will create the certs. Update your path to private and public on your SAMPLE-server.js(server.js) file.
You would only run node SAMPLE-server.js (you will want to change this to server.js for actual deployment).
This file will automatically take care of running the other two websites.
Note: to keep it running use forever start server.js. If you don't have that, run npm install -g forever