In the edit map foldout you will find everything you need to modify your map.
When generating a map randomly you can specify how many layers should be added in the settings tab.
TileWorldCreator generates the base map randomly and adds for each layer the same map to it, but with an inset.
The inset value can be edited in the settings.
You can assign one preset for each layer.
To add a new mask layer, select the layer you wish to apply a new mask and click on add mask. To know more about mask layers see: Working with mask
It is recommended to switch the scene camera in Unity to orthographic and the view to top. Right click on the menu underneath the axis view in the scene editor. Also make sure to be in the move tool in Unity before painting(W)