The Process Entire DEM menu option will map subcatchments for all defined subcatchment outlet locations and display their boundaries. This algorithm is the most time intensive since it effectively determines the flow path properties for every pixel in the DEM.
It is only necessary to undertake flow processing in areas of the DEM where the subcatchment mapping may have changed. Thus, if one subcatchment is being further discretised (Subcatchments >> Breakup Subcatchment) then it is only necessary to reprocess flow paths for that subcatchment (Subcatchments >> Reprocess Subcatchment). Running the DEM wide flow processing option should only be necessary after defining the major catchment outlet or making wholesale changes to the DEM.
Another way to speed up this algorithm is to clip the DEM to an area only slightly larger than the catchment of interest. Use the DEM Conditioning>> Miscellaneous >> Apply Clip Mask to DEM and import a polygon GIS file with which to clip the DEM. This effectively causes all pixels outside the first polygon in the GIS file to be removed from the DEM.