Seperation Faction Plug-ins

Hey Everyone, I need someones help. Im Currently working with A faction server owner to make a OP Faction server. But, the only way he said he will allow me to make the OP faction server is if i can figure out how to separate the 2 faction plugins from each other. He has a Normal Faction's world and wants to separate the factions from the other world. What is the Code or How do i separate faction plugins from each other? I also could be looking for a Plugin Manager to help me build things and make sure they work together. Not everything is set in stone yet but Ill Take applications.