The results of density functional calculations are reported for RuGe and RuSn model clusters, with Sn and Ge atoms located either at a high coordination site (central location) or at a low coordination site (corner location). The model clusters have been first studied at a fixed bulk geometry. Then, in order to simulate small bimetallic particles, their structures have been allowed to relax. The relative stabilities of the model clusters support the conclusions that the most stable aggregates are those where Sn and Ge are located at low coordination sites. However, when relaxation occurs, the clusters distort in order to accommodate Sn or Ge at the center of the first layer. This distorsion induces a reduction of the coordination of this central atom. The relaxation effects stabilize the RuGe particle, with Ge at both sites, leading to only a small preference for the corner site. At the opposite, the distorsion necessary to accommodate a central Sn atom costs too large amount of energy, which leads to a large preference for Sn to segregate at a corner site. Quantum chemical calculations are shown to be very helpful in order to quantify the cluster distorsions and the site preference effects when Ru is replaced by Sn or Ge.