Works perfectly fine both ways, depends on what format the ISO is and the layout of it
Dave the Man is asking for the same thing I did a number of posts back, basicly a list of what files you have for the ISO, this will help us help you run the ISO without the need of D-Tools and such, though D-Tools is a very handy tool to have anyway for other CD based game system emulators like Saturn and Playstation and many others