I would try to find a holistic way to get rid of the stains, before using Angel Eyes. It contains tylosin which is a low-grade antibiotic. A bit harsh to use on a puppy, plus it's expensive stuff. Others here use water and hydrogen peroxide mix I think, they will chime in soon..
Your best bet for the staining is to change the food. You mentioned he has runny poo, how long has this been going on? The antibiotics could be the cause if it's short term, but if it's been continuous then it's the food.