Social distancing, vaccination, and medical treatments have been extensively studied and widely used to control the spread of infectious diseases. However, it is still a difficult task for health administrators to determine the optimal combination of these strategies when confronting disease outbreaks with limited resources, especially in the case of interconnected populations, where the flow of individuals is usually restricted with the hope of avoiding further contamination. We consider two coupled populations and examine them independently under two variants of well-known discrete time disease models. In both examples we compute approximations for the control levels necessary to minimize costs and quickly contain outbreaks. The main technique used is simulated annealing, a stochastic search optimization tool that, in contrast with traditional analytical methods, allows easy implementation to any number of patches with different kinds of couplings and internal dynamics.