My question is how to encode php codes but I am not looking for a site to do it ( or a program ) . I am asking how to encode manually ? I mean how to change out codes into an unknown string so others may not understand what our codes are .
If you're looking for a compiler to compile your PHP code into byte code and add some obfuscation so that others cannot gain access to your code. Here are a few:
Some (if not all) of these compilers have features to obfuscate your code.
More at Can you "compile" PHP code?