Set aside about 5-6 chips to top each muffin ( 60-72) and stir the rest into the batter.
This recipe makes 12 largish muffins using a regular-sized muffin pan with the wrappers filled nearly to the top with batter. But, you can also stretch it out to make about 18 muffins (as shown in this post) when sticking to the 3/4 full of batter standard.
And in case you're wondering what protein powder, flax seed and wheat germ I use, check the bottom of my post for links. I actually get the wheat germ in the cereal aisle at Food Lion but the other two from Amazon.