Well, maybe you could have a single .xml file, but make the WebUI (or the
possible future CoreDaemon) to allow "partial" dowloads/uploads.

It's an XML file, so the CoreDaemon could be capable of "give me only the
<shaper> object" or "Take the <shaper> I'm uploading and mix it into  your
config.xml". That is, you don't split the config.xml, you can still
down/upload it on one piece, but you can also work only with small peaces of
it ;)

c u.
Marc.