Summary: We provide effective and practical guidelines on the choice of the complex denominator function of the discrete derivative as well as on the choice of the nonlocal approximation of nonlinear terms in the construction of nonstandard finite difference (NSFD) schemes. Firstly, we construct nonstandard one-stage and two-stage theta methods for a general dynamical system defined by a system of autonomous ordinary differential equations. We provide a sharp condition, which captures the dynamics of the continuous model. We discuss at length how this condition is pivotal in the construction of the complex denominator function. We show that the nonstandard theta methods are elementary stable in the sense that they have exactly the same fixed-points as the continuous model and they preserve their stability, irrespective of the value of the step size. For more complex dynamical systems that are dissipative, we identify a class of nonstandard theta methods that replicate this property. We apply the first part by considering a dynamical system that models the Ebola Virus Disease (EVD). The formulation of the model involves both the fast/direct and slow/indirect transmission routes. Using the specific structure of the EVD model, we show that, apart from the guidelines in the first part, the nonlocal approximation of nonlinear terms is guided by the productive-destructive structure of the model, whereas the choice of the denominator function is based on the conservation laws and the sub-equations that are associated with the model. We construct a NSFD scheme that is dynamically consistent with respect to the properties of the continuous model such as: positivity and boundedness of solutions; local and/or global asymptotic stability of disease-free and endemic equilibrium points; dependence of the severity of the infection on self-protection measures. Throughout the paper, we provide numerical simulations that support the theory.