A .raw file (or .sav file) contains all the information needed to perform load flow calculations and is the electrical model of the system.
A .sub file is used to define smaller "subsystems" within the larger load flow system in the .raw file. The .sub file accomplishes this through defining groups based on certain load flow characteristics: areas, buses, voltage levels, etc. This is then used to create a DFAX file for ACCC analysis. More information about this is in the "Linear Network Analysis" portion of the Program Operation Manual, or search for "DFAX".
For example, imagine you are performing contingency analysis with different voltage criteria between the HV and LV networks. This can be specified through thoughtful combinations of the .sub file and the .mon file. Overall the "sub" file helps one to focus in on the results within the area of interest and can cut out lots of noise from electrically distant portions of the case.