Is there a problem with the Mother? I just wondered why you wanted them in with the Father. I think normally the pups stay with the Mother until about 3 to 4 weeks (Souffle will know exact times), when you separate the girls from the boys. I think generally they do better separated from the Mother, with girls in one cage, boys in another, Mum in another cage, when the pups are old enough. The Father needs to be removed as soon as the babies are born or, as Souffle says, the Mother will get pregnant again.
If you did put any pups in with the Father it could only be boys or he could mate with the girls. I don't think I would risk it personally, if the Father is already separate. A bit more info would help people advise
