HECRAS will model in a mixed flow regime, therefore, one can cut xsecs to match the physical characteristics of the plunge pools. I have modeled plunge basins as energy dissipators in HECRAS and obtained very close results when compared to the design for energy dissipators. On the other hand, I have ignored the basins and filled in the holes using a much reduced manning's roughness to represent water. I would recommend that you model it and look at the results to see if they make sense. If you can defend your model then you're done.