There are two ways to setup a EB-Server. You can use the ingame GUI to create a listen server or a dedicated server.
To choose this way might cause problems sometimes the game will freeze or just close when you are creating the server.
A much safer way is to use the DedicatedServer.bat that you find in your UT2004/EikoBattle directory, it can also be found in your start menu under EikoBattle/EB-Server. This file will run a dedicated server on your computer. The map list and other variables will be based on your last successfully dedicated server's info.
If you want to change the setup of your server right click the .bat file and choose "edit".
You will see this text:
@echo off

@echo on
@echo Starting Dedicated EikoBattle server
@echo EikoBattle by PigBear
@echo -------------------------
@echo off
:10
cd ..\System
ucc server EB-Invasion.ut2?game=Eiko.EikoGame?TimeLimit=20?MinPlayers=0 -mod=EikoBattle -LOG=EikoBattle.log
copy server.log EBServerLog.log
goto 10

The first parts are not interesting, it only writes text in your command prompt.
this line:
ucc server EB-Invasion.ut2?game=Eiko.EikoGame?TimeLimit=20?MinPlayers=0 -mod=EikoBattle -LOG=EikoBattle.log
will start the server. We will take a look at the different parts of the command line.

cc server EB-Invasion.ut2?game=Eiko.Eiko Game?Time Limit=20?Min Players=0 -mod=EikoBattle -LOG=EikoBattle.log
This part chooses what map will be played FIRST, it can be replace by any map name.
The map name's are:
EB-Chain2.ut2
EB-City.ut2
EB-Horror.ut2
EB-Office2.ut2
EB-Sehr.ut2
EB-Ruin .ut2
EB-Invasion.ut2
For more info on maps check out the Maps-section.

ucc server EB-Invasion.ut2?game=Eiko.EikoGame?TimeLimit=20?MinPlayers=0 -mod=EikoBattle -LOG=EikoBattle.log
The to int numbers represent the two other variables that can be set.
The first TimeLimit=20 sets the time limit (in minutes) if no team has 0 Eiko after this amount of time the one with the
most Eiko will win. Its best to have a time limit because EikoBattle games can go on almost forever.
The second , MinPlayers=0 ,is also an int. It represents how many players that MUST be in the game.
For example if its set to 4 and 2 persons connect to your server, the other two players ( to make 4 ) will be bots.

ucc server EB-Invasion.ut2?game=Eiko.EikoGame?TimeLimit=20?MinPlayers=0 -mod=EikoBattle -LOG=EikoBattle.log
These parts just makes sure that the GameType is right and that EikoBattle is loaded. The log -part makes the log be saved as EikoBattle.log this log is found in your UT2004/EikoBattle/System folder.

Most of the old ut2k4 server commands still work, check out:
http://unreal.epicgames.com/servertips.htm
for more info on commands.