We present neutron and synchrotron powder-diffraction investigations as well as ab initio calculations to elucidate delicate structural features in doped skutterudites. Samples with assumed Fe doping were investigated (FeyCo4Sb12, y=0.4, 0.8, 1.0, and 1.6), as well as samples with formal Ni substitution (Co4-xNixSb12, x=0, 0.4, 0.8, and 1.2). The present study serves as a case story for the determination of fine structural details of thermoelectric skutterudites by diffraction methods in combination with ab initio calculations. We illustrate the problem of fluorescence in the conventional x-ray powder diffraction on the Fe-doped samples by a comparison with the neutron powder-diffraction data. On the series of the Ni-substituted samples, the neutron powder-diffraction data were collected to investigate the exact sitting of the Ni. The sample with the highest Ni substitution (Co2.8Ni1.2Sb12) was also used for high resolution, high-energy synchrotron powder diffraction measurements. These revealed that the sample consists of two skutterudite phases. A complete description of the Ni-substituted samples was obtained in tandem with ab initio calculations, which show that the system contains a Ni-rich (Co0.38Ni3.62Sb12) and a Ni-poor (Co3.76Ni0.24Sb12)) skutterudite phases.