If you haven´t already, please consider adding
- search field for link to existing document, as exists on iOS
- search field for preferences
Thanks.
The way linking works on iOS is adjusted to suit the interface limitations. On the Mac you can freely drag and drop items around, which makes for a more flexible system overall. One of the many things you can do when dragging an item is drop it into a text editor to create a link to it. As for the search interface, try the one that is right in the main toolbar: Quick Search. It works a bit like the iOS search field does. True it is an open-ended tool, you can do many things with the search results, but one is to drag the result and drop it. 
With preferences, try searching in the user manual. The topics that discuss features will often refer to any available preferences that modify the core behaviour, and of course Appendix B itself goes over the whole list, and can be searched as text.