A model system of partial differential equations in two dimensions is derived from the three-dimensional equations for thermal convection in a horizontal fluid layer in a vertical magnetic field. The model consists of an equation of Swift-Hohenberg type for the amplitude of convection, coupled to an equation for a large-scale mode representing the local strength of the magnetic field. The model facilitates both analytical and numerical studies of magnetoconvection in large domains. In particular, we investigate the phenomenon of flux separation, where the domain divides into regions of strong convection with a weak magnetic field and regions of weak convection with a strong field. Analytical predictions of flux separation based on weakly nonlinear analysis are extended into the fully nonlinear regime through numerical simulations. The results of the model are compared with simulations of the full three-dimensional magnetoconvection problem.