Small cell networks are the key to the success of the next generation wireless systems because of the potential huge capacity gain, but pose many challenges on managing the inter-cell interference from huge number of small cells and that from macrocells. Recently, an interesting technique, called interference alignment (IA), was proposed to align the mutual inter-cell interference (ICI) in the same sub-space by designing the beamforming vector among the coordinated cells. Because of the reduced ICI, the system capacity of an IA system can be improved. Nevertheless, the methods of selecting a group of users for the IA system has been rarely seen in the literature, especially in the macrocell/small cells hierarchical overlaying networks. In this paper, we investigate the effects of pairing users and base stations in an IA-based hierarchical overlaying macrocell/small cells networks. Furthermore, we design an IA scheme that can not only reduce the inter-cell interference among small cells, but also avoid interfering with the overlaying macrocell. Comparing to the conventional IA scheme based on the random pairing for users and base stations, the sum rate of the proposed joint user scheduling and IA beamforming design is 30% and 64.5% improved for the cell edge users with the SNR-based and SINR-based pairing for the users and base stations.