First off, I don't own a roadster but this is my opinion and others can chime in that may have an electrical backround. I don't see it a problem operating the top either way. My preference would be to use the top with the engine running (alternator charging). That way you are running the pump motor at a higher voltage (maybe 2 volts more) causing less amperage to operate the motor, and less wear and tear on the motor.

If I am wrong, please someone correct me.

James