Doctors in KKH's children department are all qualified and accredited. I would not think there will be a difference in terms of qualifications, but there might be more volume of patients over at the children's hospital as compared to a PD.
Regardless of which one you choose, it's better to stick to the same doctor so they will be more aware of the social and emotional issues of the child in addition to his medical history.
http://www.kkh.com.sg/Services/Children/GeneralPaediatricsandAdolescentMedicineService/Pages/Home.aspx