The default .appcf files are in the "app" folder within Editor/PE. According to Help Center "set appconfigfile" topic, you can use "set appconfigfile" to force a certain file to be used. If you use a simple filename for that command, it will search inside the custom folder for the current doctype, either at the root level or in the "app" folder.
Using .zip file deployment works just as regular custom folders, the only difference is Arbortext will download, unzip and manage the custom folder location.