How do I get the watch to automatically record reps when doing crunches?

The watch relies on the accelerometer to detect reps. If your hands are in such a position as to not detect movement, then the reps will be zero or less than your actual number of reps. I do crunches with my arms crossed and the watch is usually pretty close. Also, I prefer to setup the exercise so that it ends upon lap button press. That way when you're done you can edit the reps if necessary.