There are many ways of doing this. The main point is that your thinking (algorithm) is not correct. There will be essentially be an encrypt function and a decrypt function.

A layer on top of that is that the number of bytes sent == number bytes received by some protocol. This is like receiving a binary file with a "checksum".

By definition of an encrypted link, there is NO comparison of sent byte 1 to received byte 1. Ie, I sent a "secret message", you get it and decrypt it, but there is never any discussion about whether my char 3 is the same as char 3 that you sent. In fact, I may even send more encrypted bits (or even less) than you sent me to encrypt to begin with!

Typically the encrypted message is "transported" via standard protocols that show the num bytes sent, etc. You "got" the encrypted message by: 1)transport layer says that it is ok (number of bytes sent and received are the same and reasonable probability that no transmission error occured, 2)decrypted values "make sense".