He won't have any conflicts with anything in the GS as long as he goes to the control panel and sets slot 6 to "Your Card" so that it will check the slot to see what is in there. Also if he sets the Startup Slot to 6 then it will automatically boot from the Disk II drive that he has hooked up to the controller card in the slot.
Since the majority of software expects to boot from slot 6 I'm not sure anything he tried to boot would run since it's expecting slot 6.
Dean
Dean