First get rid of the fleas. Consult your vet because if the irritation is from the fleas, then the vet can give you medicine to help with the itchies.

If the problem persists when the dog does not have fleas then it is possibly an allergy. My Dusty has allergies and he chews his fur whenever he is in a flair up. Flea control and other topicals irritate his skin so he only gets them if necessary. Fortunately he has not had fleas so eliminating the flea products hasn't been a big headache for us (yet). He does get brewers yeast which I believe helps prevent fleas naturally.

Your best source of help is your vet.