We consider the problem of designing integrated mathematical models for staratum fluids filtration and gas-liquid mixture flows (i.e., oil, natural gas, and water) in oil- and gas-gathering pipelines. The modeling process lies in finding a generalized solution to an initial boundary problem for a system of equations describing real physical process in oil and gas strata, shafts, and ground-based gathering pipelines. We suggest and study methods to solve the systems of nonlinear algebraic equations defined by the space-time approximation of the initial boundary problems belonging to the class considered.