Good evening - I'm Dr. Sara. I'm a licensed veterinarian who works exclusively with dogs and cats. Based on your description, I think you're referring to perianal fistulas, which is a common and very frustrating problem with German Shepherds.
Perianal fistulas are a weird inflammatory disease in dogs that is still somewhat of a mystery. They are easy to diagnose on examination and predictable in their refractory nature - meaning that they can be very difficult to treat. My experience with using prednisone has been pretty poor - it does work for a little while but not very well, and the lesions always recur when we stop therapy. Plus prednisone can have some really significant long term side effects.
Atopica (modified cyclosporine) has a great success rate in putting lesions into remission and keeping them clear. Since the disease is chronic, unfortunately, the dog has to stay on the medication for life. The dosage is adjusted to the lowest dose that keeps the lesions under control - this is variable but usually in the range of two to three times a week, although sometimes I do have dogs that require dosing every day to keep their fistulas under control.
Some dogs will respond well to a hypoallergenic prescription food like Iams Response KO or Royal Canin hypoallergenic select protein diets, while for other dogs, the diet doesn't seem to have an impact. Other dietary tweaks that work for some dogs include varying the amount of fiber in the diet. I also recommend probiotics for all of my patients who have inflammatory conditions, as they help regulate the body's immune function overall. My favorite probiotic is FortiFlora - it is packaged in box of 30 packets - one packed is sprinkled on the food each day.
Another medication that can be helpful either in conjunction with the Atopica, or potentially by itself for small or mild lesions is an ointment called tacrolimus. Tacrolimus is applied directly to the lesion daily and it can control small lesions alone, or help control larger lesions when used in conjunction with the Atopica.
One last treatment we use quite frequently is laser therapy. Laser therapy is directly anti-inflammatory to tissues and also produces good local pain control and wound healing. Laser therapy sessions last 5-10 minutes and are performed two to three times a week initially and then spaced out to a less frequent maintenance schedule or potentially stopped all together during times when the dog has no active lesions.
As you can see, there are a number of options that you've not yet explored, so I hope that this gives you some information to keep in mind the next time you discuss your girl's lesions with your vet. Please let me know what other questions I can answer for you :)