It is a difficult concept to understand and I tried to simplify it as much as I could and tried to avoid the details. I have taken a few years of physics and different kinds of calculus in my short life and I still have to pause and think about the difference before I write it out. Both are important when talking about an arrow, but momentum is what you use to figure out the penetration because it is a vector and is directed into the animal's side, while the friction is working against it by pointing out the animal's side along the same axis as the arrow. The net force resulting from combining these vectors is what determines penetration (how long it takes for the velocity of the arrow to reach zero).