It sounds as if you want Epeiros as Pergamon not as your own but as an AI faction.
If so all you need to do is :
1. Get the Force Diplomacy mod and make whomever is controlling Pergamon hand it over to you
2. Give Pergamon to Epeiros while demanding all their settlements
3. Give Epirote settlements to whom you want to live there in their stead ( if, as you write, you want rebels you should just leave the cities undefended, but be aware that, though avoidable, a CTD is likely if they all rebel at the same time. The first couple of times they will surely rebel back to the previous owner but destroy any buildings that decreases squalor and send in spies and eventually it will belong to the slave faction )
4. Move Epirote FM´s and armies via the show_cursorstat and the move_character "Firstname middlenameLastname" console commands.
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