i would suggest to use a mild anti itch dog shampoo (maybe once a week) to get out the dead skin, then i would get a skin sample at vet for investigation
there are many reasons from fungus to mites - if u want a better opinion here u should upload some pics of the areas if its visible
did u regular clean the resting places? (i would suggest to put easy to clean blankets on them and change them every 2-3 days to no dead skin debis build up there, then wash them as hot as possible with mild cleaner)
and maybe change the dogfood for some allergic ones couldnt hurt