If you use the -configsubdir parameter on your server command line that launches your game, eg -configsubdir=Ro2DEDpublic , then your ini files are copied into rogame\config\Ro2DEDpublic when the game next starts/restarts.
When you do a hlds update to the rogame, only the default ini files are updated. This seems to work for us.
The Web admin "finds" the game based on the ip address -multihome=126.96.36.199 and the port number ListenPort=8080 in ROweb.ini you dont need to do anything else.
Play around with it on your pc first though!
... if your using Fire Daemon...