First of all you need csv file with cards, usually missing cards are promo cards, which actually exists in another set but were reprinted in some specific set, in this case only fields you need are: NAME|SET|ARTIST|COLLNUM|IMAGE_URL.
In Card Navigator view select Import button, select Extend database options in the bottom and select csv file to import.
When you press Finish it will tell you that set does not exist and you should create a new set and enter abbreviation for this set. Then your cards should be in the database, and you can add them to your collection or decks (as separate step).To add set you have to add a line in tables/editions.txt in the folder mentioned above definining properties or the set or you can do the same from UI by going to Window->Preferences->Magic Preferences->Card Sets-> button Add...
Then you create a set as .xml file with the name of the set but where all non-letter symbols are replaces with _ (underscore). For example Urza's Legacy is called Urza_s_Legacy.xml. Open any of these file to see example of the format. Once you done both steps and restart the app it should pick up new set. The good example is Anthologies.xml - this set is only one that I ship which is not connected to gatherer online database. It shows how to set images URL. Cards id's have to be negative too (positive are used for gatherer now). Html tags in text fields have to be escaped (like <br>)