I had a pretty detailed post on the oldforums (can't we get them hosted on someones old 8086 or something?).
Anyway...
After installing the server, from the command prompt navigate to your alleg server directory, type
allsrv -service to run as a service.
To edit the servers values run regedit, navigate to; HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft Games\Allegiance\1.0\Server
Edit > New > DWORD Value
Right click value and rename to
ASGS_RANKS_ON
Right click value and modify Value Data to
1
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If you want server to autoupdate, right click CfgFile and Modify to
http://autoupdate.alleg.net/allegiance.cfg
by default servers do NOT autoupdate, and are pointed here;
http://autoupdate.alleg.net/AllegianceServer.cfg
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To add a core;
Edit > New > String Value
Right click and rename to Core# (where # is the next core in sequence you've set up, 1,2,3 etc.)
Right click and modify to change the actual core file to be used, do not use periods, do not add igc, for example... ("RTc006a").
Edit > New > String Value
Right click and rename to Game# (where # is the next game in sequence you've set up, 1,2,3 etc.)
Right click and modify to give the displayed name for the core in the lobby, try and use the same naming conventions for current cores, also try and include the version info. The version is important as people might update at different times.
Make sure core1 is matching game1, as core1 is loading the core file and game1 tells everyone what the game file is.