First. you need to decide if you want a centralized server or a peer-to-peer system. If you want a centralized server, you have all of the users connect to your server via AJAX, WebSockets, etc. If you decide to use peer-to-peer you can use the Multiplayer plugin which runs through Scirra's signalling server. The signalling server is a temporary connection to serve as a meeting place for game clients to connect directly to one another, so it is not a persistent connection.
If you choose to do a centralized server, you need to select a language to write your backend programs in. Java, Python, PHP, come to mind and design an application program interface for your server and game clients to communicate by and choose a protocol to communicate with (HTTP, AJAX, WebSockets, etc.).
Key words to google:
centralized, peer to peer, api, application program interface, session management, authentication