The following are the initialization files I used in setting up my server. The trick for me was to not modify anything unless it needed modification. For me, the axiom "if it's not broke, don't fix it" was the rule of the day. Everything in RED is what I changed from the default.
This is the master initialization file, automatically created by the server upon its first run. It's probably the most important file you'll use. So...BACK IT UP! This is especially true as some of the official Bonus Packs will write over this file upon install.
This is the initialization file used by UT2Vote49. This file supersedes UT2004.ini in many instances, so check here for changing files before UT2004.ini. You may notice (as I did), that many of the changes you'll make in the WebAdmin interface will not take effect. This is because they're controlled by this file, which in come cases is not modified by the WebAdmin interface.
This is the batch file that calls the ucc.exe executable for running the server. As with many batch files and executables, it needs some startup parameters. You'll notice that my runserver.bat has text calling "AccessControl=XAdmin.AccessControlIni". This "controls" the WebAdmin. For my server, I setup several different Administrator classes. I have true, global Administrator privileges. I have given my friends limited Administrator privileges so that they may modify the current game but not the defaults. This prevents my .ini file from accidentally being....wrecked. This "AccessControl=XAdmin.AccessControlIni" line calls the next .ini file, XAdmin.ini, where the usergroups and users are defined.
As described above, this file defines the users and usergroups used within the WebAdmin interface.