via In-Game Interfaces. It suggests you permissions based on installed plugins,
visualises permissions checks and manages your chat all in one interface.
Note: These gifs are outdated.
Automatically view available permissions based on installed plugins
Can also manage Bungee Permissions and can use MySQL for Storage
Basic Chat Manager is already included
Timed Groups & Permissions
Add temporary groups & permissions to players
Add Groups or Permissions only for specific servers and worlds
Can be fully controlled via commands which can also be used for automation