IIRC the issue with Applied Cryptography was that while it was the best resource for learning the math behind different crypto systems work and how to implement different algorithms it gave almost no guidance about how to actually use them in the real world. Which led to a lot of people deploying insecure systems based on just reading AC.

My understanding is that Cryptography Engineering and Practical Cryptography address this and focus on using crypto in the real world rather than mathematics and theory.