If he isnt neutered then marking is normal..is he the father of the pups? If you have used him as a stud then the marking will probably be a permanent thing now,so I sugest belly bands whilst hes indoors as some breeders say that studs dont make good pets so they have to be confined.I have friends with male dogs that mark and its a habbit they dont usually get out of once they start.I would get some belly bands