It kind of depends on the acidic strength of the AF as to if you neutralize or not, and personal preference. If the iron used to make the AF is no longer reacting, it most likely doesn't need to be neutralized. Having said that, I personally neutralize even weak solutions, just my preference.
Typically, you neutralize after the stock has been blushed with heat. Either household ammonia, or a baking soda solution (baking soda + water) is a good choice.
Ed