The variational multiscale method has been shown to perform well for large-eddy simulation (LES) of turbulent flows. The method relies upon a partition of the resolved velocity field into large- and small-scale components. The subgrid model then acts only on the small scales of motion, unlike conventional LES models which act on all scales of motion. For homogeneous isotropic turbulence and turbulent channel flows, the multiscale model can outperform conventional LES formulations. An issue in the multiscale method for LES is choice of scale partition and sensitivity of the computed results to it. This is the topic of this investigation. The multiscale formulation for channel flows is briefly reviewed. Then, through the definition of an error measure relative to direct numerical simulation (DNS) results, the sensitivity of the method to the partition between large- and small-scale motions is examined. The error in channel flow simulations, relative to DNS results, is computed for various partitions between large- and small-scale spaces, and conclusions drawn from the results.