Animal and robotic collective behaviours can exhibit complex dynamics that require multi-level descriptions. Here, we are interested in developing a multi-level modeling framework for the use of robots in studies about animal collective decision-making. In this context, using robots can be useful for validating models in silico, inducing calibrated repetitive stimuli to trigger animal responses or modulating and controlling animal collective behaviour. However, designing appropriate biomimetic robotic behaviour faces a major challenge: how to go from the collective decision dynamics observed with animals to an actual algorithmic implementation in robots. In previous work, this was mainly done by hand, often by taking inspiration from human-designed models. Typically, models of behaviour are either macroscopic (differential equations of the population dynamics) or microscopic (explicit spatio-temporal state of each individual). Only microscopic models can easily be implemented as robot controllers. Here, we address the problem of automating the design of lower level description models that can be implemented in robots and exhibit the same collective dynamics as a given higher level model. We apply evolutionary algorithms to simultaneously optimise the parameters of models accounting for different levels of description. This methodology is applied to an experimentally validated shelterselection problem solved by gregarious insects and robots. We successfully design and calibrate automatically both a microscopic and a hybrid model exhibiting the same dynamics as a macroscopic one. Our framework can be used for multi-level modeling of collective behaviour in animal or robot populations and bio-hybrid systems.