Facial hair shouldn't be too much of a problem when applying topical treatment, so long as the hair isn't too long. Just make sure you apply it well onto the skin and get under the hair.

I have a beard but my most problem area is my forehead (I don't do anything to my beard area except wash and condition it). Keep in mind BP bleaches hair (and towels, shirts, pillows, ugh...) If you're trying to treat acne that is under a beard then it is best to keep it shaved off because it is hard to get creams beneath it and the excessive rubbing that is required will cause an extreme amount of irritation.