Methane dynamics in a water-saturated soil layer with gas-transporting roots is modeled with a weighed set of single-root model systems. Each model system consists of a soil cylinder with a gas-transporting root along its axis or a soil sphere with a gas-transporting root at its center. The weights associated with a different cylinder or sphere radius were deduced from root architecture. Methane dynamics in each single-root model system are calculated using a single-root model from the previous paper. From this full model a simplified model was deduced consisting of an oxygen-saturated and an oxygen-unsaturated model system. An even more simplified model was deduced, called the homogeneous model. In this model the concentrations are homogeneous in the whole soil layer. Simulation results of the simplified model are closer to the simulation results of the full model than the simulation results of the homogeneous model. The overall effect of the simplifications on simulated methane emissions are small, though the underlying processes are affected more severely, depending on simulation time and parameters. At high root densities and at large times, under stationary conditions, root density is proportional to simulated methane fluxes, provided that carbon availability is proportional to root density. Sensitivity analysis shows that lack of knowledge on root gas-transport is an important limitation for the predictability of methane fluxes via the processes at the kinetic level.