Many mesoscale cloud simulations of grid spacing O(1km) employ a turbulent-closure model for subgrid-scale mixing as well as a numerical spatial filter to avoid numerical errors. In this study, the effects of mixing by subgrid models and numerical filtering in simulations of mesoscale cloud systems are investigated using the newly developed Weather Research and Forecasting (WRF) model. Because the WRF model's numerical scheme is free of numerical filters, we have been able to examine the sensitivity of squall-line simulations to the parameters in popular turbulence-closure schemes and to the parameters in the numerical filters (which were added to the WRF model for this purpose). The basic test case is the three-dimensional development of a line thermal in a moist unstable, no-shear environment. In this case the simulated flow is composed of thunderstorm cells forming and dissipating along a line. This study was motivated by our initial attempt to simulate this flow using the WRF model's 5th-order upstream differencing scheme for the advection terms along with a widely used 1.5-order TKE scheme. Using this combination of advection scheme and turbulence-closure model, the solution was characterized by many poorly resolved grid-scale cells. However, by increasing the proportionality constant C in the eddy viscosity coefficient, the cells became well-resolved; but further increases in the constant overly smoothed the cells. Such solution sensitivity was not noticed in previous cloud models as they have typically used numerical filters that were responsible for most of the needed smoothing at small scales. We have performed a series of simulations with the WRF model using 3rd- and 5th-order advection schemes and, for comparison with the original Klemp-Wilhelmson cloud model, a 4th-order centered scheme with a 4th-order filter. We find that, as compared with the scheme using a 4th-order filter, the upstream schemes using subgrid models with a viscosity coefficients 1.5 to 2 times larger than those normally used, retain more power in short scales, but without an unwanted buildup of energy.