Cumulus parameterization is recommended for domains with a grid size greater than or equal to 10 km. You likely would not need to use cumulus parameterization below 3 km. In between 3 and 10 km, you would need a cumulus scheme that's aware of the smaller grid sizes.
Explanation
A cumulus scheme considers atmospheric conditions that are conditionally unstable and sub-saturated, while a microphysics scheme is only active in a grid volume that's saturated.
Cumulus schemes are designed for grid spacing large enough that cumulus clouds are consistent to occupy only a portion of the grid box, hence when the grid size becomes smaller, the scheme may be replaced by explicit clouds on the grid.
Any time you make modifications to your configuration - using a different compiler, netcdf, versions, paths, setting new environment variables you would like to incorporate into your compilation, or when you make modifications to the registry files, you must clean and reconfigure before recompiling. If you only make modifications to any other files (e.g., physics routines), you can simply issue the compile command, and it should not take nearly as long as a full compile.