The difference is in usage. Apa=what Apa yang dia makan? What does he/she eat? Dia makan apa? (in English it literally means He/she eats what?) Makan apa dia? (in English it literally means eat what he/she?) In the context above you can't say "Apa dia makan? Because it changes the meaning which is "Does he/she eat?" In this case the word apa doen't mean what but simply the informal form of apakah. Hope this helps.