Set options in batch file during installation

[SamHills]

I use a batch file to configure Windows and install a standard set of apps, including ExplorerPatcher. I need to put something in this batch file to set some of the properties (options) which do not default to what I want them to be. This can be a config file, registry edits, or anything else that can be put in or called from a batch file as part of the EP installation process. This must be completely automatic - no user interaction required.