Hello Harvliet Dalgety,

Yes, you should define certificate files in config.json and then you will be able to run the server and use it for many sites. 

Problems may occur if you install Jot Server on server without certificate and then try to use link from this server on https (secure) sites, in this case all requests from https sites will be blocked by your browser, because in most cases browsers don't allow to load not secure content (http) to secure sites (https).

Well, in your case everything should work fine for all sites, because your server on https (secure) server, you just need to define path to certificate files.