PermissionsEx is a permissions plugin based around giving players access to certain things. Every plugin has certain commands and every command has a certain permission to it. To be able to access that command you need that permission for that command. These are called permission nodes. They usually look like this.

permission.permissionnode.test

The basic plugin mainly everyone has on a server is Essentials. Lets say you wanted to give your players access to a certain command
throughout permisisonsEx

You'd type a basic PermissionEx command.

Command You Are Gonna Be Giving A Group: /Home
Example: /Pex group <group> add <permission node>
Usage: /Pex group default add essentials.home

Now you are going to get an error within permissionsEx if you try to type this in game. That's normal. 
When you first load up permissionsEx it generates a default file, in your servers plugin folder. You are gonna wanna go inside this
config and look for "allow-ops: false" and change it to "allow-ops: true" so this means your operators in game (admins) can use permissionsEx through commands, instead of accessing the console. Then try to retype the command as before then it should be good. If the permissions doesn't apply you can type "/Pex reload" and this will reload the permissions plugin.