Hax's Great Guide to Civil War

[Hax]

E.g. if I am Epirus, and want my Epirote rebels to use the Koinon Hellenon faction slot (greek_cities), does that mean I have to wipe out KH first? Or should I leave at least one KH city (e.g. Rhodes) alone before I make the modding changes? Or will bringing a 'dead' faction back to life this way mess up the EB script?

No, the faction you use to rebel has to be alive with at least one city, somewhere. It won't work with dead factions at all.