first get the ja dedicated server program from jk3files.com, im guessing you will be using the win32 version of it. then, enable your router to let information for ja to pass through (mine is automatic, so if you have a probelm here you need to find someone else). next, you need to configure your router. you will need to set it so that the ports 29070-29099 are forwarded to the pc you are running the server from. you then start the program, and it should work like that. theres a lot more you can do with a server though, but its best no to try to much at once.
are you going to run the server from one computer and play on another? and is this for the internet?