As an update, the 1.1 version went live today and the CustomDice directory can be somewhere else now. I haven't updated the documentation for it just yet but after you run the new version of the app., there will be a file called "settings.set" saved in the app data folder (a folder beside or inside the app).
inside the settings.set will be a list of properties, change "CustomDiceDirectory" to be the location you want for your custom dice folder. You can also set it to "*" (without the quotation marks) to save dice in a directory relative to the app, should you want to carry the program around on an externam drive :)