This is a pretty broad question. You should always store your model data in a model object of some kind, be that a Core Data entity, an NSMutableDictionary or a custom object of your own creation. You should definitely NOT be storing the data in an NSTreeController or NSOutlineView instance, these are not model objects.
If you're using Core Data for the rest of your app and you need to persist the data that is manipulated by the outline view then this is a good choice, but it might be overkill if you have only simple requirements.
To control what is displayed in the outline view you can either use NSTreeController or your own controller object that responds to the NSOutlineView datasource and delegate protocols. In practice you might use both, as some things such as whether or not an item is a group item can only be controlled by the NSOutlineView delegate methods.
In my personal experience I've found that NSTreeController can be very difficult to deal with for anything beyond very simple tasks and I now longer use it, I find it's much simpler to just use the datasource methods in my own controller.
As far as modifying the contents of the outline view, you should always modify the model via a controller, you should never update the view directly. You would implement methods such as -add: in your controller or use the -add: method of NSTreeController if you're using it.
Your view's controller should then detect the change in the model and ask the view to update. The view controller and model controller can be the same object but they don't have to be. Key-Value Observing is a useful technology that can inform your controller of a change in the model.
Here's some sample code from Apple that you might find useful:
http://developer.apple.com/mac/library/samplecode/SourceView/
http://developer.apple.com/Mac/library/samplecode/AbstractTree/