My female was showing allergy symptoms. I changed the food, and was successful in eliminating most of the symptoms except the ear scratching.
I cleaned the ears REALLY thoroughly with mineral oil and q-tips, then applied Surulan to the ear, making sure the exposed part of the leather was treated as well as deeper inside the ear.
Symptoms improved right away!
Even if there is no infection, scabs from scratching fall down inside the ear and irritate it. The problem becomes self-perpetuating.
I'm one of those people who's not afraid to clean really deep inside the ear. It saves the expense of the vet doing an ear flushing. Here's what I do.
(These instructions are not aimed specifically at the OP, who says her dog has been checked for infection and ear mites.)
Find a nice, sunny spot in the house. Get a bunch of Q-tips, some mineral oil and some paper towels or tissues. Soak both ends of the Q-tips in the oil, then set them aside. Put some oil on a tissue or towel, wrap it around your finger, and wipe the inside of the ear as best you can. You'll be surprised at how much dirt there is. Don't be upset if you see blood. You've probably just dislodge a scab from a small cut the dog caused when it was scratching, or you may be dealing with ear mites, which are usually the other cause of bleeding! (The reason I'm so good at this is we had a cat for 17 years. And for 17 years, he had ear mites, so his ears needed regular cleaning about once a month!)
Then, use the Q-tips to clean out all the nooks and crannies you couldn't reach with the paper towel. Carefully go deep inside the ear canal, too. It's over an inch long, and a lot of dreck can get lodged down inside there, and cause horrible itching. If the dog is fairly co-operative, you may even be able to see it, with the help of the bright sunlight.
I know doctors say not to use Q-tips, but I've been doing this for over 40 years, both with my own ears and my pets, and have yet to cause any damage.
If the ear has a foul or yeasty odour to it, you are dealing with an infection, and you need to take the dog to the vet for treatment.
Finish off by applying Surulan (or other veterinary ear drop) to the inside of the ear. Make sure you treat the upper part of the ear (the part you can see easily when the ears are erect) as well as the ear canal. If you don't have ear drops, and the ear is very inflamed and raw from scratching, some polysporin ointment would help. A hydrocortisone ointment, available over the counter, will also help reduce inflamation and itching. Don't put ointment deep inside the canal, though, as, unlike eardrops, it will likely stay there and may interfere with the dog's hearing. Just apply it to the visible raw spots.
The main problem with ear care is most people just want to get it over with as quickly as possible, and they just shoot some eardrops into the ear, without really LOOKING at what is going on! If there's visible dirt there, you need to CLEAN it! A dirty ear, full of scabs, wax, and ear mite excrement is NOT going to stop itching, no matter what you do to it!