The GEOPAK Files related to the project you work on are going to be stored in your Working Directory which you specify once you are in a DGN file under GEOPAK>User Preferences. You navigate to the folder you want and it holds that folder til you change it. Many GEOPAK dialogs allow you to browse to a file anywhere on your computer network so files can be placed anywhere but it starts with the Working Directory as the root. There is no need to edit configuration files to achieve this behavior.
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