All permissions, with a description and a default value, can be found in the PermissionDefaults.yml file. Open it using a text editor and you can view an hierarchical view of all permissions of the plugin. In here you can freely change the default permission value (op/not_op/true/false) for all permissions the plugin uses. A server reload or restart is required for new permission nodes to take effect.
Sometimes so-called 'variable' permission nodes exist. They are, by default, shown with a main name followed up by a * node. These nodes allow additional sub-permissions to be added, or represent a permission for a certain world, player or some other name. An example of a such a permission can be found below:
myplugin: use: '*': default: op description: Can use all tools hammer: default: true description: Can use the hammer tool drill: default: false description: Can use the drill tool
In the above example, OP players can use all tools. This includes the drill! All players can use the hammer, but no one can use the drill. Note that the false default is usually pointless, because not-added variable permissions are false by default anyhow. Generally you would want to add either true or op as default for these sub-permission nodes. (hammer and drill)
The nodes in the file correspond to the permission nodes you can give to players. In the above example, you can use the permission node 'myplugin.use.hammer' to allow a player to use the hammer. If you wish to give someone the use for all tools, you can use 'myplugin.use.*'. Again, the nodes in PermissionDefaults.yml are defaults; you can override them for individual players or groups.
If you wish to use a permission plugin that doesn't use Super Permissions, you can install Vault to redirect the permission handling. BKCommonLib automatically detects when Vault is enabled and will switch to using Vault for permission handling.