Orthographic Encoding refers to methods and rules by which a language is written. This includes the rules for spelling, syntax, punctuation, etc. that are agreed upon to make a written language a vehicle for clear and precise communication.
For instance, in English we have many homophones (words that sound alike but mean different things depending on how they're spelled), such as to, too and two where each has its own meaning. Improper use of these spellings can turn a written sentence into nonsense. i.e "I went two the store too by to oranges." In English it is also important to use punctuation and word order correctly, or it can drastically change the meaning of a sentence.