Hi there! Running a ScrumbleShip server isn't all that tricky, but there are a couple of gotchas.
Linux (Or other unix-alike) is an absolute requirement for running the ScrumbleShip server as of June 2013. Dirkson will take patches for other OS support, but the time libraries are currently linux-only. Dirkson STRONGLY recommends running the server software only on server grade OSes - Linux, BSD, etc.
First off, you should create a new user for your ScrumbleShip server. This ensures that any exploits or problems in the server software can't affect anything but the ScrumbleShip server.
Once you've set up your user, grab the linux scrumbleship bundle, copy it to your server and unzip it in the user's directory. This may seem wasteful, but the server actually uses a lot of data from the client config directory to do its job.
Change into the scrumbleship directory and run "scrumbleserver". Immediately shut it down again with control+C. The server will have made a text file called "serveroptions", which you should edit.
Here's a rundown of the current options:
Address - What IP address to bind to. For many servers, "0.0.0.0", which means "any", will do fine. If your server has multiple IP addresses, you'll need to specify which one ScrumbleShip should listen on, otherwise Scrumble will listen on the first IP address only.
Port - What port to use. Currently the client is hard-coded to port 18150
MaxAsteroidSize - The maximum size of asteroids on your server. This number can be raised or lowered.
Players - Maximum number of players. Currently unimplemented.
Once you've edited the options, run your server again. Congratulations, you've set up a ScrumbleShip server!
Currently there is no server command line, and the server will not fork itself. Those wishing to keep the server up indefinitely should use a looping script and "dtach" or "screen".
For your users to connect to your server, they'll either need to edit their options file and change "ServerURL", or run ScrumbleShip like this: ScrumbleShip.exe yourserver.com Username