Crypto implementations bits and bytes Reading many papers in the homomorphic encryption domain and in cryptography, a lot of schemes operate on bits as 1 and 0. 

If I wanted to implement a scheme, for example, Gentry's FHE, would I have to encode inputs as "bits" or just use bytes (C &amp; C++ (char), Golang(byte), etc)?
That issue is not really relevant when one implements such schemes, because the plaintexts are typically used only in the encryption, where they are combined with big values that need to be encoded as big integers anyway.

All the homomorphic operations should not depend on the plaintext, so, the chosen encoding is irrelevant here.

And even if the decryption outputs a single bit, all the operations done in the decryption function are performed also over big integers.

As an example, the scheme implemented by Leo Ducas uses a regular C integer to encode input bits, as you can see in lines 29 and 30 of file LWE.h from his Github repository.