Hydrograph does have a rudimentary chamber option for underground basins. It assumes simple pipe with options for header and stone encasement. For small sites with underground chambers, I prefer HydroCAD. Haestad Pond Pak would be another option.
p58 of the 2007 manual describes underground chambers with open contour pond above, but I never figured out how to do it.
If you have an odd size underground basin with just some underground storage or the brick shaped blocks, I calculate the total storage manually, then enter as contours and adjust percent void to match the total volume.
The most important thing for me would be to verify that underground chambers allows infiltration out of the bottom. I do most of my routing to obtain a volume infiltrated value for NPDES permits.
Ann Wingert, P.E.