Here are the parts I have and I don't know how to put them together so things correctly point to the right places

• A server with VestaCP running
• 2 domain names registered with Godaddy
• 1 IP address (came with the server mentioned above)
• Cloudflare

Goal is to have both domains use same ip address and webserver will direct traffic to the correct public_html folder on server.

In Godaddy update nameservers to use Cloudflare NS. Then use Cloudflare to configure A records. A record is the IP that you have. 

Then set up virtual host with apache and provide correct Documentroot for each website.

 https://httpd.apache.org/docs/current/vhosts/examples.html