The master configuration file is openGLCD_Config.h
openGLCD is shipped with ks0108 configuration files that are similar to the configuration files in the GLCDv3 library. The default pin mappings and wiring used with the GLCDv3 library will work with openGLCD since the default pin configurations is the same.
Normally, for a standard 128x64 ks0108 panel, the only changes necessary for a custom pin configuration will be to modify the ks0108_{BOARD}.h file. Everthing else will automatically configure itself.
If the custom configuration is more complex than simple pin changes to a 128x64 display:
In terms of how to actually move a custom pin configuration from the GLCDv3 library to the openGLCD library, it has to be done manually. Each pin from the GLCDv3 pin configuration file will have to be manually moved into the openGLCD pin configuration file. The pin names used in pin configuration files in openGLCD are very similar to those used in GLCDv3. The difference is that all pin names now include the term "pin" in them.
See the library configuration page for full details on configuration: Configuration