If your using FL Studio u can automate the on/off switch of the of any of the plug-ins (not just fruity) by opening up the FX channel u are using and then right clicking on the little green dot next to the FX u want to switch on/off. Then click 'edit events'

Then u draw in the automation data as you would with any other automation. Bar all the way up means the lug-in is on, and the bar all the way down turns it off.

hope this made sense to you, and hopefully helped a bit