Might want to take a look at this: Frog Forum - Fruit Fly Culture Lid Modification.

Myself just pour the flies into a clean extra 32 oz. plastic container. You can return some to culture cup if accidentally pour too many and also add your supplement powder to it and dust the flies. A second 32 oz. container can help separate flies from supplement powder and then you pour the right amount of dusted flies to enclosure without pouring powder from dusting into it .