So uh... how exactly do I do that? I'm confused on how the server actually works since it's just a window, doesn't really give me any info.
If you run it by double clicking, then you only see a mini window.
This means that the server is running, and you can connect to it. To save game data and stop the server - simply close the server window.
If you want to have more control over the server - then you need to run it from the command line.
Example:
java -jar d:\tachyon\server\TachyonServer.jar
You can connect to your own server with either of these:
Used ports are:
TCP 30303
UDP 30304
Also if you start the server with a console, then you can even see when someone connects to it.
Whenever there's a new connection to the server - it shows this in the console logs.