Depends on where the file resides but basically you can just edit any file or registry when in packaging mode and Appvolumes will register that setting, even permissions will be saved.
So in your case both options work. You can either copy the file into the appstack or change the file. If the file however resides in the c:\Users part of the machine it wont be captured using Appvolumes, because Appvolumes cannot capture user settings. You would either need to place in in the all users folder or you need to use DEM to get those files there.