When you run Phex headless, you won't be able to change anything. It just allows you to run it in background without being able to do anything (yet).
With the changes in the releaseline-3.x branch, you can simply restart it with GUI, and the statistic of uploaded files will show you, what happened while Phex was headless
I can't really help you on the sharedlibrary, since I also don't know how it's layout works.
Modification of xml files might even be inefficient, since Phex only outputs its settings there - afaik it doesn't read them out while it runs.
I know that this is a quite limited headless mode, but I hope it's still useful
PS: Sorry for replying so late... I didn't see your post
Thanks go to only a hobo, who pointed me to the thread.
PPS: Do you have some ideas how to get the wiki more structured?