Go to Assignments, right click the button you want to change, 'assign new action', go to keystroke and there you have it. As if cue wouldn't support modifiers :D.
With the FN key it is different though.
The FN keystroke is not being sent to windows so it's up the drivers from the laptop manufacturer to interpret the signal.
So you would have to find different hotkeys to do what the FN key does (see Media Control in the assign menu, win+p to change to presenter mode etc.)