I have done several duathlons and have never seen this run-bike-run-bike-run format before. As you likely already know the 1st mile or so of the run after the bike can be a challenge... and you get to do it twice in one race :-) Makes it even more important to get your brick workouts done in training.

I'd go with the clip-in pedals as you should make up the extra 20 or 30 seconds it will take to change your shoes over the 20 miles of riding. I agree with Bart; practice, practice, practice.