Say you have a battery with a round-trip efficiency of 80%.  HOMER assumes the charge efficiency is equal to the discharge efficiency, meaning they are both equal to the square root of 80%, which is 0.894.  So if you put 100 kWh of DC electricity into the battery (assuming it could absorb it all) then the energy level in the battery would increase by 89.4 kWh.  Then if you discharged all that energy, you would end up with 80 kWh of DC energy back on the DC bus.  The energy level of the battery would have increased 89.4 kWh, then decreased by 89.4 kWh.  So the throughput from that event would be 89.4 kWh.