Well, the easiest thing to do would to put the config data in a sub folder, have the wyUpdate.exe and client.wyc in that subfolder and have a separate wyBuild project for that config data. This way updates can be done on the config data while your program is running.
Of course you'd have the separate wyBuild project for your main app (and the main app's wyUpdate.exe and client.wyc would be "base directory").
Lastly, if you want to simplify things you can use a single wyUpdate.exe (in the main app's base dir), then pass in the config folder in the -basedir commandline option and the config project's client.wyc file using the -cdata commandline option.