For sorting your media, MediaTomb supports custom scripting using JavaScript. For some examples, check here: http://mediatomb.cc/dokuwiki/scripting:scripting
Regarding the vob-files: I don't use vob-files so I don't know but I think you're looking in the right direction (the config.xml).
I know MediaTomb supports DVD-images (as of version 0.12) so it should be able to also use the vob-files.
Edit: you found the scripting examples already
