Before beginning a game, make sure you specify which options you prefer. Once the game has begun, you should not use the Options menu (it will behave unpredictably). The "Ghost Deck Setup" button is the last step before beginning a game. For example, you might take these steps...
Also note that some options are mutually exclusive, but this mod does not enforce that. For example, if you select "Kung-Fu School (only)," don't follow that with either "White Moon" option (White Moon already includes the Kung-Fu School) or weirdness may result.
The game should mostly be intuitive using right-click menus and some clicking and dragging. Always be sure to right-click a piece or card before trying an alternate method, just to make sure (generally useful VASSAL advice).
You drag ghosts off the deck to "draw" them. Moving them barely off the deck to any open space in the bottom left lets you see them before they hit the board; then you drag them to where they should go, and the log will provide a helpful message about each ghost's effects. Only some functions/effects are automated, and this is (hopefully) noted in the log entry for that action.
In many cases, there are multiple "background" keystrokes firing for a single game "action". If you "undo" an action, be aware of this and click "undo" until the game is at the state you expect (in other words, don't just assume that one "undo" click will be sufficient, though in many cases it is).