it would be 아파요. I am also learning Korean, but what I learned is that when a verb stem's last vowel is ᅡ or ᅩ then you add -ᅡ요 to the end. 으 is a neutral vowel so you replace it with the ᅡ요 ending which is how you get 아파요 (아프다 -> 아프 + 아요 -> 아파요). added note: If the verb does not have a ㅏ or ㅗ vowel before the 으, then you would add the -ㅓ요 ending. Also, since the 으 vowel is neutral it is sort of "covered up" by the ending when you conjugate it. so if you wanted to conjugate 쓰다 (to use; to write) it would be 써요 (쓰다 -> 쓰 + 어요 -> 써요). Hopefully that all makes sense :)

it should be 아파요 the other option doesn't even gramatically exist.