At what point aren't you designing your own cryptosystem? Even if you use NaCl you must store your keys, determine when and when not to encrypt, decide how to g

At what point aren't you designing your own cryptosystem? Even if you use NaCl you must store your keys, determine when and when not to encrypt, decide how to generate nonces, pick between symmetric and asymmetric ciphers. I understand strongly that you should work with as large a black box as you can afford, but it becomes increasingly grey as you move toward operational stuff over "obvious" crypto stuff.