PermissionsEX permissions editor with a nice modern UI style which is easy to use and to understand! Go to http://permedit.totalh.net to begin!
When you first open PermEdit you will be presented with a popup window asking you for the permissions.yml content, but if you want to start creating one from scratch you can click "Load default".
To load your permissions.yml into PermEdit you simply open plugins/PermissionsEx/permissions.yml with a text-editor of your choice. Then copy all the contents into the Permissions.yml text-box on the website and click "Load".
When you have loaded your YML you will be presented with a list over all groups and a menu on top where you can open the list of users. In the group list you can click on "Create a new group" to open a popup where you can create a new group. If you click on a group in the group list or a user in the user list you will open a popup where you can edit the name, prefix, suffix and permissions of that group or user (You cannot edit the name of a user).
When you are done editing your permissions you can simply click "Export" in the top menu to open up the load menu with your updated YML code in it. Simple copy this into your permissions.yml file found in plugins/PermissionsEx on your server and run /pex reload to load the new configuration.