In order to add moves using YAPE, you need to remove moves from existing pokemon. Check the evolutions, as most have moves that are on their move list twice (at Lv 1 and after)
Maybe you don't understand my problem that well. I'm editing a non existing one. I am not overwriting any Pokemon. But the ones that appear as 2 question marks can only have 1 attack they learn without HM or TM. This is a big problem since I will have 4th and 5th gen Pokemon you get from egg and they will only be able to learn 1 attack. So what you said wasn't my problem. I have no interest of changing moves on existing Pokémon. Only the non existing.