JUst like with humans, long term antibiotic use is bad.
I use a product called 'eye envy' and it worked great at removing my boy's slight stain as a puppy, now i use it 2-3 times a week as preventative(i always use liquid and powder). It comes in a small kit, but lasts very long. I've had my 'EE Starter Kit' for 3.5 months now and it looks barely used.
www.eyeenvy.com
I assume since you have been using angel eyes your dog does not have set in stains, so this would be a great product to use after baths once your dog is dry. I find the powder really boosted the power of the liquid and would never go without it. Also another great tip is to cut the application pads in half if your dog has long hair, and into quarters if short hairs. I feel the pads are big and work just as well cut to double the number of applications.