SSL for pointed domains

I have an app that is "multi-domain", Other domain just have to point to the IP address to run on my app on the web-server.

Using letsencrypt, I have also generated SSL for those pointed domain using "HTTP" challenges.
Now, my problem is – how do I tell my webserver to read that generated SSL files for the pointed domain.

They are not hosted on my server with config settings. They are just pointed with the IP address to my App and My app renders the content based on a domain name.

• I am using VestaCP to manage server, domain, and email
• Pointed domains have no config file on my server. They work on the web-application level.

How do I set https for that pointed domain? On a note, I already have valid SSL files – just not sure, where to post or point them, since there is no config.

Can they be kept using "htaccess" or at a web-application level?

E.g, My app runs at "http://example.com" and shows content for example.com, and for the second domain that is pointed to my server "http://anotherExample.com" – my app shows the content for "anotherExample.com" and so on and so forth. "example.com" is hosted on my server with Nginx and apache config, so SSL is set. But anotherExample.com is not hosted on server level but only at the app level – now, where do I set SSL for it? I have already successfully generated SSL using letsencrypt with HTTP challenge.

Update: I run a platform like Blogspot.com Multi-Domain blogs – How to serve SSL for pointed domain?

Thanks

server {
  listen         *:443 ssl;
  server_name   domain1.com;
  ssl_certificate /path/to/domain1.crt;
  ssl_certificate_key /path/to/domain1.key;
  ...
}

server {
  listen         *:443 ssl;
  server_name   domain2.com;
  ssl_certificate /path/to/domain2.crt;
  ssl_certificate_key /path/to/domain2.key;
  ...
}