A default rawproc.conf is installed in the appropriate Windows directory. In it, you'll find a slew of configurable items, such as the tool defaults, control point sizes, and logging. You can add or delete these with a text editor, then run rawproc to see the changes take effect. The Edit->Properties dialog allows you to change parameter values while rawproc is running.
If you run rawproc from the command line, you can make a separate rawproc.conf in the working directory and rawproc will use it instead of the installed file.
The input and output parameters are a special case - each configuration parameter holds a semicolon-separated string of name=value pairs. Right now, the only available parameter outside of the extensive set of raw parameters is for JPEG output file quality, quality=P, where P is an integer between 0 and 100. The list of available parameters is a separate help topic.