I don't remember having any config file yet but you can modify the source code
I just wanted to be able to redirect McChunk to a different folder instead of having the world in the same folder. This won't be a huge problem for me soon, I guess 'cause I'm moving my folder and everything anyways. But it would have been nice before.
Also, endenizen has a fork https://github.com/endenizen/MC-Chunk-Loader in which he has updated the PHP server-side code to handle region files also and done some other improvements. I will have to work on incorporating that.