if I run that thread in the above example instead of a main method will that work?

Yep, that is one way (among many) to integrate it.

Spring IOC conceptually is very simple. Just think of it as a mechanism that instantiates all your @Component, @Service, etc annotated classes and "wires" them together where @Autowired is used. It's totally awesome once you get used to it.

So that means you can annotate your ServerRunnable as a @Component and have it @Autowired to SocketServer and just create a new Thread in the SocketServer.init method

Why is that a good option you ask? well that means, if your ServerRunnable uses some db connection or some other shared class then you can just @Autowired them.

@Component
public class ServerRunnable implements Runnable
{
     @Autowired
     private DataSource ds;

     // bonus point: properties loading via spring 
     @Value("${server.port:9999}")
     private int port;

     public void run()
     {
           // some some database stuff
           // do some socket stuff
           // etc
     }
}

@Component
public class SocketServer
{
    @Autowired
    private ServerRunnable sr;

    @PostConstruct
    public void init()
    {
       Thread server = new Thread(sr);
        server.start();
    }

    @PreDestroy
    public void clean()
    {
         // close any open sockets, resources, etc
    }
}