If you want to add new stuff that gets created as the game is played, put it in the $game... objects instead.
If you want to create your own data that is unrelated to the data files, you'll need to create your own $data... objects and a corresponding json file that gets set up outside of the engine/editor, and you'll need to update the new game, load game and save game functions to include these.
If you want to add new data to the existing structures, like actors, classes, states, just use the note box for it, and make your plugin read the notes like many others do. Some databases, such as Tilesets, Animations and Systems, don't have note boxes though so you'll need to go with the previous method.
My current use case is adding additional message fields to States, so every player character gets a different message when they're hit with the same effect.