Cabinet mode is really what you want and you can request a code from Zen right from the Pinball FX 2 or FX 3 menu.
However if for some reason you do not wish to use cabinet mode you can select the grid positions of your games in the Game Manager and enable non cabinet mode support in PinballX
To enable non cabinet mode of FX in PinballX simply remove the table parameter from the FX2 or FX3 settings. Also ensure you are using PinballX 2.42 or above.
So for example:
-applaunch 442120 "-table_[TABLEFILE]"
Then ensure you select the grid positions of your installed games in the Game Manager. PinballX will then send keys to FX to navigate the games.