It makes no sense to me to choose a zero drop shoe and then add cushioning. Are you planning to run part of the way without the cushioning? If not, perhaps a walking shoe with more cushioning on the heel would be a better choice.
However, if you have already bought these, you might consider using a full length replacement footbed like those from Superfeet. Or you could keep your current footbed and just use a heel insert like Scholl's Orthoheel. I have used both approaches. The choice somewhat depends on how good the OEM footbed is - if it has reasonable padding, there is less need to replace it and just use a heel insert.