If you have multiverse and create multiple worlds, your permissions plugin (i.e. I use Group Manager) SHOULD automatically create a seperate folder for the world you create, identical to the main world one.

Example:

My main world: World
it would have its own folder containing its own groups and players config files

Second world (for the sake of names...) We'll call it Olympus
A folder identical to the world file would be created, however it would be called Olympus.
Olympus would have its OWN group and player config files, which are unconfigured such as how you first installed your permissions managing plugin would have been. Configure to your liking and you're done. It's fairly simple.