+set fs_game <modname>   that is: +set fs_game instagib

For example: 

  quake3.exe +set dedicated 2 +set fs_game instagib +set bot_enable 0 +exec instagib.cfg

You have several options for the config file. You can place it in the baseq3 directory as usual or you can place it in the mod directory. For example: c:\quake3\instagib\instagib.cfg The batch file will execute it in either place but it will execute only the one it finds first. So dont have duplicate names of files in both directories. Its probably a good idea to put the mod server config files in the mods directory. 

Some mods like Weaponmod create other settings files and place them in another directory. You can usually change this around. For example when running weaponmod it creates a settings file in a settings directory. Once you've created your settings file, you can place it in the same directory as the server config file and execute it from the config file. For example, at the end of the server.cfg file, place the command: 

      /exec weapmodsettings1.cfg 

and it will do so. This can be more efficient to make sure the settings file does get executed properly.