Following Part I, in which 3-D cloud-resolving model (CRM) simulations of a squall line and mesoscale convective complex in the mid-latitude continental and the tropical regions are conducted and evaluated, we examine the scale-dependence of eddy transport of water vapor, evaluate different eddy transport formulations, and improve the representation of convective transport across all scales by proposing a new formulation that more accurately represents the CRM-calculated eddy flux. CRM results show that there are strong grid-spacing dependencies of updraft and downdraft fractions regardless of altitudes, cloud life stage, and geographical location. As for the eddy transport of water vapor, updraft eddy flux is a major contributor to total eddy flux in the lower and middle troposphere. However, downdraft eddy transport can be as large as updraft eddy transport in the lower atmosphere especially at the mature stage of mid-latitude continental convection. We show that the single updraft approach significantly underestimates updraft eddy transport of water vapor because it fails to account for the large internal variability of updrafts, while a single downdraft represents the downdraft eddy transport of water vapor well. We find that using as few as 3 updrafts can account for the internal variability of updrafts well. Based on evaluation with the CRM simulated data, we recommend a simplified eddy transport formulation that considers three updrafts and one downdraft. Such formulation is similar to the conventional one but much more accurately represents CRM-simulated eddy flux across all grid scales.