According to various studies, researchers have found that stability ball crunches activate greater muscle activity when compared to regular floor crunches done without a ball.
But you'll get the greatest muscle activity in your abs when performing stability ball crunches where the ball is placed as far down on the lower back as possible (near your lower lumbar region). Stability ball crunches with the lower back resting on the ball, can be TWICE as effective as to crunches performed with the upper back resting on the ball. Also perform the exercise slowly for maximum benefit.
Stability ball crunches where the ball is placed under the upper back, may not actually be as beneficial as regular floor crunches. So if your just starting out, you may want to start with the stability ball near your upper back to perform crunches, and as you progress and get stronger, move the position of the stability ball towards your lower back.
Overall, abs workouts that use a stability ball will engage the smaller core muscles more and show greater muscle activity of your six-pack muscles (a.k.a the rectus abdominus).