It should be just as simple as selecting Network timer -> Server mode, then typing a user name and hitting "Start Server" on one machine. Then doing Network timer -> Client mode and typing a username and the IP of the host machine, then click "Connect to Server."
If the host machine is using a router to connect to the internet, you may have to set up port forwarding on the router. It shouldn't be too difficult.
To test the functionality though, you can just run 2 instances of JNetCube on the same machine, and point the client to 127.0.0.1 .
Granted, I don't have JNetCube to test with, but I am using JTimer, which is just an overhauled/updated version of JNetCube.
Any number between 1 and 65535 should work in theory, generally avoid from 1 -1024 though. This number needs to be the same on the server and the client.
If you're really interested as to what they do, there's plenty of places to find out. It really doesn't matter though as long as they are the same on the client and server. And if you need to set up port forwarding, as I mentioned earlier, this number becomes much more important as you have to make sure that whatever port number you select is also forwarded through your router to the host machine.