Hello, I am making red velvet cupcakes, covered in fondant, with a cream cheese center. Now i know your'e supposed to refrigerate cream cheese frosting, but I also know you're not supposed to refrigerate fondant. My question is, will the cream cheese icing be safely "stored" inside the cupcake? what should I do?

As long as the cc frosting will be eaten within a day, yes it'll be fine 'stored' in the cupcakes without refrigeration. The sugar acts as a sort of preservative. DON'T add milk to the frosting.