I would take separate samples. Even thought they live together they might have different levels in their systems. Different levels of parasites require different levels of medicine. You wouldn't want to be overdosing or underdosing one of them.
Make sure you bring a fresh sample. Best case scenario, put both of them in warm water right before you leave for the vets. As soon as you see them lift their tails to poop, scoop them out and let them poop on a paper towel or something. Bag the samples up, put the babies away and drive to the vet.
