Spelling relates to how to write one or more words with letters and diacritics. Punctuation relates to the symbols that indicate the structure and organization of written language, as well as intonation and pauses to be observed when reading aloud. Clearly, both spelling and punctuation are aspects of orthography, but orthography also includes other elements such as hyphenation, capitalization, and emphasis.
Clearly there's an overlapping, but the three tags can coexist: questions about orthography in general could be tagged with two tags: orthography and the tag associated to the specific aspect of orthography addressed in the question. For example, spelling-related questions could be tagged with both the spelling and ortography tags; simmilarly, questions about punctuation could be tagged with the punctuation and ortography tags. Those questions relating to the other aspects of orthography (hyphenation, for example) can be tagged with orthography and a (possinly new) hyphenation tag.