How long does he have this trouble?
Is the hair loss in the edges or the very top of his ears?
I am sorry your baby is having trouble.
There is an ear dermatitis specific to doxies which may be the culprit.
You can read about it here:
Treatment consists of first washing her ears with a non allergic shampoo.
Selsun blue works well in these cases.
Then apply plain neosporin three times a day.
She is much better off on a natural food than science diet so you made the right choice.
If you think this is a allergy related give her one mg per lb of benedryl.
I hope your baby feels better very soon.
Warmest best wishes,