In “cad é atà tù a dhèanamh”, “cad è” is the direct object of the verb. When your word is the subject or the direct object of the verb, you use the direct relative.
In “cén chaoi a bhfuil tù”, which means “what (is) the manner that you are”, “manner” isn’t the direct object nor the subject, it’s something else, so you use the indirect relative.