I wonder if Cryptography Engineering, while updated, is a good book as Applied Cryptography, that really was a pretty inspired one.
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.
This is funny, because an old buddy of mine who did a brief stint at the NSA let slip that they almost never compromise the algorithm, it's virtually always the implementation where the weakness lies.
Always the easiest path, defeat the implementation.