OK, the HBV is vacuum operated and without vacuum (engine off) the position of the valve is such that it allows flow through the heater matrix. When vacuum is applied, it bypasses the heater matrix.
This probably means that you can plumb the pre-heater into the circuit where the pump currently is and it will work fine, since it only runs when the engine is stopped.
As to the direction of flow of the pump, I ditched mine a long time ago so I can't check but, if it only operates with the engine stopped, I guess it probably doesn't matter which direction it pumps.
If the climate panel is configured not to have the pump installed, the pump runs all the time, I believe. Could it be that the climate panel has been swapped, or maybe it has the wrong config?