I'd imagine that everyone would want to run it fullscreen. Could you simply change the instructions that appear on first run to say that this run will create the appdata folder, then instruct the user where to place the files, and indicate that the configuration will automatically take place on the second run of the PND, when all required data files are in place? I know there's a general push on here to try make usings software as painless as possible, so avoiding having to edit config files would certainly be easier for most!