First and foremost, be calm. The fundamentalist viewpoint thrives on emotion and passion. no matter how stupid of offensive it might get, maintain an attitude of scientific dignity. Don't be afraid to express emotion, of course, but don't let it get the better of you.
I'd also recommend a little research ahead of time. Specifically, what are the primary arguments he'll be using, and how do you defeat them. Preparation and information are the best friends of science.