Changing the morphology of the growing surface and the nature of residual impurities in (Ge,Mn) layers - by using different substrates - dramatically changes the morphology of the ferromagnetic Mn-rich inclusions and the magnetotransport properties. We obtained p-type layers with nanocolumns, either parallel or entangled, and n-type layers with spherical clusters. Holes exhibit an anomalous Hall effect, and electrons exhibit a tunneling magnetoresistance, both with a clear dependence on the magnetization of the Mn-rich inclusions; holes exhibit orbital MR, and electrons show only the normal Hall effect, and an additional component of magnetoresistance due to weak localization, all three being independent of the magnetic state of the Mn rich inclusions. Identified mechanisms point to the position of the Fermi level of the Mn-rich material with respect to the valence band of germanium as a crucial parameter in such hybrid layers.